Use of tgf beta superfamily antagonists and neurotrophins to make neurons from embryonic stem cells

ABSTRACT

This invention provides a system for efficiently producing differentiated cells from pluripotent cells, such as human embryonic stem cells. Rather than permitting the cells to form embryoid bodies according to established techniques, differentiation is effected directly in monolayer culture on a suitable solid surface. The cells are either plated directly onto a differentiation-promoting surface, or grown initially on the solid surface in the absence of feeder cells and then exchanged into a medium that assists in the differentiation process. The solid surface and the culture medium can be chosen to direct differentiation down a particular pathway, generating a cell population that is remarkably uniform. The methodology is well adapted to bulk production of committed precursor and terminally differentiated cells for use in drug screening or regenerative medicine.

RELATED APPLICATIONS

This application is a divisional of pending U.S. utility applicationSer. No. 09/888,309, filed Jun. 21, 2001 (docket 090/002), through whichit claims priority to the following U.S. provisional patentapplications: U.S. Ser. No. 60/213,740, filed Jun. 22, 2000 (Docket090/001X); U.S. Ser. No. 60/213,739, filed Jun. 22, 2000 (Docket091/002X); U.S. Ser. No. 60/216,387, filed Jul. 7, 2000 (Docket092/001X); and U.S. Ser. No. 60/220,064, filed Jul. 21, 2000 (Docket091/003X). This application is also a continuation-in-part of U.S. Ser.No. 10/873,414, filed Jun. 21, 2004 (Docket 094/012p).

The following patent applications are hereby incorporated herein byreference in their entirety: U.S. Ser. No. 09/888,309, filed Jun. 21,2001; U.S. Ser. No. 60/213,740, filed Jun. 22, 2000; U.S. Ser. No.60/213,739, filed Jun. 22, 2000; U.S. Ser. No. 60/216,387, filed Jul. 7,2000; U.S. Ser. No. 60/220,064, filed Jul. 21, 2000; U.S. Ser. No.60/175,581, filed Jan. 11, 2000; U.S. Ser. No. 09/688,031, filed Oct.10, 2000; U.S. Ser. No. 09/718,308, filed Nov. 20, 2000, U.S. Ser. No.60/257,608, filed Dec. 22, 2000; International Patent ApplicationPCT/US01/01030, filed Jan. 10, 2001; International Patent ApplicationPCT/US01/13471, filed Apr. 26, 2001; and U.S. Ser. No. 09/859,351, filedMay 16, 2001.

TECHNICAL FIELD

This invention relates generally to the field of cell biology ofembryonic cells. More specifically, it relates to conditions that allowhuman pluripotent stem cells to be directly differentiated into cells ofa particular lineage, suitable for applications such as use in tissueregeneration and the screening of biologically active substances.

BACKGROUND

Recent discoveries have raised expectations that stem cells may be asource of replacement cells and tissues that are damaged in the courseof disease, infection, or because of congenital abnormalities. Varioustypes of putative stem cells differentiate when they divide, maturinginto cells that can carry out the unique functions of particulartissues, such as the heart, the liver, or the brain.

A particularly important discovery has been the development ofpluripotent stem cells, which are thought to have the potential todifferentiate into almost any cell type. The next challenge indeveloping the technology is to obtain dependable conditions for drivingdifferentiation towards particular cell lineages that are desired fortherapeutic purposes.

Early work on embryonic stem cells was done in mice (reviewed inRobertson, Meth. Cell Biol. 75:173, 1997; and Pedersen, Reprod. Fertil.Dev. 6:543, 1994). Most methods of differentiating mouse pluripotentstem cells involve three strategies, often in combination:

-   -   Permitting the cells to form aggregates or embryoid bodies, in        which cells interact and begin to differentiate into a        heterogeneous cell population with characteristics of endoderm,        mesoderm, and ectoderm cells. The embryoid bodies are then        harvested and cultured further so that the differentiation can        continue.    -   Inducing the cells to differentiate using soluble factors that        promote particular forms of differentiation, optionally with        simultaneous withdrawal of factors that inhibit differentiation    -   Transfecting the cells with a tissue-specific gene, that has the        effect of directing the cell towards the tissue type desired

Mummery et al. (Cell Differentiation Dev. 30:195, 1990) comparedcharacteristics of mouse embryonic stem (ES) cells with two embryonalcarcinoma lines. The cells were differentiated either by letting cellsform aggregates, optionally in the presence of retinoic acid (RA) ordimethyl sulfoxide (DMSO); or letting the cells grow to confluence,optionally depriving the culture of leukemia inhibiting factor (LIF) ordifferentiation inhibiting activity (DIA) found in high concentrationsin medium conditioned by Buffalo rat liver (BRL) cells. The studysuggested that mixed endoderm-mesoderm cells were obtained afterremoving inhibitors of differentiation, and parietal endoderm-like cellswere obtained by RA induction.

Grendon et al. (Dev. Biol. 177:332, 1996) generated an endothelial cellline capable of embryonic vasculogenesis from mouse ES cells. The cellswere transfected with the early region of SV40 Large T antigen, and thencultured in medium comprising homogenized mouse testes, which promotesdifferentiation. An endothelial line was derived that expressesendothelial cell specific proteins and can be induced by basicfibroblast growth factor (bFGF) and LIF to proliferate to form vasculartubes and microcapillary anastomoses.

Van Inzen et al. (Biochim. Biophys. Acta 1312:21, 1996) differentiatedmouse embryonic stem cells by incubating the cells for at least 3 dayswith retinoic acid. The cells were cultured either as a monolayer, or asembryoid bodies on a non-adhesive substrate. The cells obtained fromculture stained positively for the neuronal markers NF-165 and GAP-43,and were electrically excitable in a patch clamp assay.

Dinsmore et al. (Cell Transplant. 5:131, 1996) report a method forcontrolled differentiation of mouse embryonic stem cells in vitro toproduce populations containing neurons or skeletal muscle cells.Embryoid bodies were allowed to form, and were induced using dimethylsulfoxide (DMSO) to differentiate to muscle cells, or using retinoicacid to differentiate to neurons. Muscle cells were also made bytransfecting ES cells with an expression vector for muscle-specificprotein MyoD.

Rathjen et al. (J. Cell Sci. 112:601, 1999, and International PatentPublication WO 99/53021) formed a primitive ectoderm-like (EPL) cellpopulation from mouse ES cells using conditioned medium from the humanhepatocarcinoma line HepG2. When grown in medium without feeder cells,but including LIF, the mouse ES cells reportedly grew as a homogeneouspopulation with most colonies displaying domed morphology.Differentiation was effected by culturing the mouse ES cells in thepresence of LIF and HepG2 conditioned medium. This gave rise to amorphologically distinct population of EPL cells with differentphenotypic markers and altered differentiation properties. EPL cellformation was reversible in the presence of LIF by withdrawing theconditioned medium.

Tropepe et al. (Soc. Neuroscience 25: abstract 205.18, 1999) reportedthat a small percentage of mouse ES cells proliferate in serum-freelow-density conditions in the presence of LIF, and form sphere coloniesthat may subsequently differentiate into neurons and glia. A smallproportion of cells from primary colonies can generate secondarycolonies independent of LIF but dependent on the factor FGF2. BlockingBMP signaling by adding noggin protein increases the proportion of cellsforming neural stem cells. About 60% of single ES cells cultured for 24h in serum-free medium express nestin.

Pluripotent Stem Cells of Human Origin

Work on human pluripotent stem (hPS) cells has been more than a decadebehind the experiments conducted on mouse cells. Human PS cells are morefragile and more difficult to isolate. Furthermore, they cannot bemaintained in an undifferentiated state under conditions developed formouse cells.

Recently, some of these challenges have been overcome. Thomson et al.(U.S. Pat. No. 5,843,780; Proc. Natl. Acad. Sci. USA 92:7844, 1995) werethe first to successfully culture stem cells from non-human primates.Thomson et al. also derived human embryonic stem (hES) cell lines fromhuman blastocysts (Science 282:114, 1998). Gearhart and coworkersderived human embryonic germ (hEG) cell lines from fetal gonadal tissue(Shamblott et al., Proc. Natl. Acad. Sci. USA 95:13726, 1998 andInternational Patent Publication No. WO 98/43679). Both hES and hEGcells have the long-sought characteristics of hPS cells: they arecapable of long-term proliferation in vitro without differentiating,they retain a normal karyotype, and they retain the capacity todifferentiate to a number of different derivatives.

Human pluripotent stem cells differ from mouse ES cells in a number ofimportant respects. Thomson et al. and Gearhart et al. maintained theirhPS cells in an undifferentiated state by culturing on a layer ofembryonic feeder cells. In contrast, mouse ES cells can be grown easilywithout feeder cells in appropriate conditions, particularly thepresence of leukemia inhibiting factor (LIF) or other ligands that bindreceptors that associate with gp130. However, LIF alone has not beenreported to prevent differentiation of hPS in the absence of feeders.Another difference is that mouse ES cells can be plated in a completelydispersed fashion; and grow quite happily to produce undifferentiated ESprogeny. In contrast, single hES cells are unstable; and propagation ofhES cells typically requires that they be passaged as clusters of cellsduring each replating.

Current efforts to differentiate hPS cells involve the formation of cellaggregates, either by overgrowth of hPS cells cultured on feeders, or byforming embryoid bodies in suspension culture. The embryoid bodiesgenerate cell populations with a highly heterogeneous mixture ofphenotypes, representing a spectrum of different cell lineages—whichdepends in part on the size of each aggregate and the cultureconditions.

Large-scale commercial production of committed precursor cells or fullydifferentiated cells from hPS cells would require a differentiationprotocol that did not involve producing cell aggregates or embryoidbodies. In addition, there is a need for cell populations that haverelatively uniform and reproducible characteristics for use in drugscreening and human therapy.

Accordingly, there is a need for new technology that facilitatesderivation of differentiated cells from human pluripotent stem cells.

SUMMARY

This invention provides a system for efficient production ofdifferentiated cells from primate pluripotent stem (pPS) cells. Ratherthan permitting the pPS to form embryoid bodies, differentiation iseffected directly by plating sub-confluent cultures of pPS cells onto asolid surface that facilitates differentiation, in the absence of feedercells or culture conditions that simulate the presence of feeder cells.The nature of the solid surface and components of the culture medium canbe chosen to direct differentiation down a cell lineage pathway that isdesired for research or therapeutic use.

Embodied in this invention are methods for directly obtainingdifferentiated cells from a donor culture of undifferentiated pPS cells,without forming embryoid bodies. Undifferentiated cells are newly platedonto a solid surface, or otherwise exchanged into a new cultureenvironment that induces differentiation of the cells into the desiredphenotype in a direct fashion, without overgrowth, aggregate formation,or otherwise creating the condensed heterogeneous cell populationcharacteristic of embryoid bodies.

One way of accomplishing this is to prepare a suspension of cells froman undifferentiated donor culture; replate and culture the suspendedcells on a solid surface so that they differentiate without formingembryoid bodies; and harvest differentiated cells from the solidsurface. A variation is to harvest pPS cells from the donor culturebefore there is overgrowth or formation of colonies; replate and culturethe harvested cells on a solid surface so that they differentiate; andharvest differentiated cells from the solid surface. Another variationis to prepare a suspension from a culture of both pPS cells and feedercells; replate and culture the suspended cells on a solid surfacewithout adding fresh feeder cells; and harvest differentiated cells fromthe solid surface. A further variation is to provide a donor culturecomprising undifferentiated pPS cells growing on an extracellular matrixin the absence of feeder cells; prepare a suspension of cells from thedonor culture; replate and culture the suspended cells on a solidsurface without the extracellular matrix; and harvest differentiatedcells from the solid surface.

A further variation is to provide a culture of primate pluripotent stem(pPS) cells that is essentially free of feeder cells; change the mediumin which the cells are cultured; and harvest differentiated cells fromthe culture after culture for a sufficient period to effectdifferentiation in the changed medium. The medium may be changed eitherby replacing the medium in the culture with a fresh medium having a newcomposition, or by adding new constituents to the medium already presentand then continuing the culture.

In any of these embodiments, the pPS cells are any type of cell capableof forming progeny of each of the three germ layers, exemplified but notlimited to human embryonic stem (hES) cells. The replating can beperformed without selecting a particular cell population from thesuspended (or harvested) cells. For example, the replated cellsuspension can be obtained by incubating the donor culture withcollagenase or trypsin or E.D.T.A., thereby releasing the cells from asurface to which the cells adhere, and collecting the released cells ina suitable medium. The replating can be done in the absence of freshlyadded feeder cells or extracellular matrix proteins on the solidsurface, such as a glass cover slip, optionally bearing a polycationsuch as polyornithine or polylysine.

Differentiation can be promoted by withdrawing serum or serumreplacement from medium, withdrawing a factor that promotesproliferation, withdrawing a factor that inhibits differentiation, oradding a new factor that promotes differentiation. Exemplary factors forgenerating neuronal cells are Brain Derived Neurotrophic Factor (BDNF)and Neutrotrophin-3 (NT-3).

A proportion of the cells cultured according to this invention maydifferentiate to precursor cells committed to a restricted cell lineageand capable of proliferation, such as ectodermal cells (for example,neuroectoderm lineage), mesodermal cells, or cells of the endoderm orvisceral endoderm. A proportion of the cells may become fullydifferentiated cells, such as neurons or glial cells. If desired, theharvested committed precursor cells or fully differentiated cells canoptionally be genetically altered with a polynucleotide that encodestelomerase.

The differentiated cells of this invention may be used to screencandidate compounds or environmental conditions that affectdifferentiation or metabolism of a cell type of interest. Thedifferentiated cells may be used to obtain cell specific antibodypreparations and cell-specific cDNA libraries, to study patterns of geneexpression, or as an active ingredient in a pharmaceutical preparation.

The differentiated cells of this invention can also be used to identifya substance expressed at a different level in committed ordifferentiated cells compared with undifferentiated primate pluripotentstem (pPS) cells. Such substances may include but are not limited tomRNA transcripts, secreted protein, intracellular protein, cell-surfaceprotein, cell-surface oligosaccharide, and particular lipids organgliosides. Expression may be compared, for example, at the level oftranscription, translation, surface presentation, or enzymatic activity.Expression of oligosaccharide and lipid substances can be inferred bychemical or antibody analysis, or by deduction from expression ofenzymes required for their synthesis. Particular embodiments involvedetermining the level of expression of a plurality of mRNAs in committedor differentiated cells made by direct differentiation, embryoid bodyformation, or any other suitable technique, and comparing the leveldetermined with the level of expression of the same mRNAs in anothercell type, such as undifferentiated pPS cells. A polynucleotide can thenbe prepared that shares sequence with mRNA that is expressed at adifferent level in the differentiated cells.

These and other embodiments of the invention will be apparent from thedescription that follows.

DRAWINGS

FIG. 1 provides an analysis of OCT-4 and hTERT expression in hES cellscultured with feeder cells (mEF) or extracellular matrix (Matrigel® orlaminin) with regular medium (RM) or conditioned medium (CM). The upperpanel is a copy of a gel showing OCT-4 and hTERT expression at the mRNAlevel by RT-PCR. The lower panel is a bar graph comparing the level ofexpression for cells grown on different substrates, expressed as theratio of OCT-4 or hTERT to the 18s standard. hES cells grown on Lamininand Matrigel® in conditioned medium have similar expression patterns tothose of cells grown on a feeder layer.

FIG. 2 is a half-tone reproduction of a phase contrast photomicrograph(10×, 40×), showing cells at various times during direct differentiationto a hepatocyte phenotype. Row A shows cells 4 days after culture in SRmedium containing 5 mM sodium n-butyrate. More than 80% of cells in theculture are large in diameter, containing large nuclei and granularcytoplasm. After 5 days, the cells were switched to specializedhepatocyte culture medium (HCM). Rows B and C show the appearance afterculturing in HCM for 2 or 4 days. Multinucleated polygonal cells arecommon. By these criteria, the directly differentiated ES-derived cellsresemble freshly isolated human adult hepatocytes (Row D) and fetalhepatocytes (Row E).

FIG. 3 is a matrix chart, representing relative expression of mRNA inembryoid body (EB) cells, compared with expression in theundifferentiated hES cell line from which they were derived. Probes usedto analyze expression are listed to the left. The first three columns ofthe matrix show the kinetics of relative expression for EB cellscultured for 2, 4, or 8 days. The fourth column (4d−/4d+) shows relativeexpression of EB cells to which retinoic acid was added for the final 4days of culture.

FIG. 4 is a reproduction of a fluorescence micrograph, showing neuronalcells obtained by direct differentiation of ES cells on a solidsubstrate using a mixture of differentiation factors. The three fieldsshown were all taken from treatments that comprised neurotrophins andthe TNF-β superfamily antagonists noggin and follistatin. A number ofcells are seen that have neuronal processes and stain for the neuronalmarker β-tubulin-III. The proportion of MAP-2 positive cells that werealso positive for tyrosine hydroxylase (a marker for dopaminergicneurons) was as high as ˜15%.

DETAILED DESCRIPTION

This invention provides a system for directly differentiating primatepluripotent stem (pPS) cells into committed precursor cells or fullydifferentiated cells. The system avoids forming aggregates or embryoidbodies as an intermediate step. hPS cells are maintained as a monolayeror dispersed from a sub-confluent pPS culture, and plated onto asuitable substrate in an appropriate culture environment that promotesdifferentiation.

Before this invention was made, the expectation was that a strategyavoiding embryoid bodies would be unsuccessful. Classical developmentalbiology suggests that interaction between the three germinal layers ofthe embryo is essential for appropriate differentiation. Embryoid bodiesare reminiscent of this early stage of development, in that they formthe three germ layers in juxtaposition.

For example, nervous tissue is formed from the ectoderm. Recent evidencefrom the expression patterns of a number of genes suggests that anothergerm layer—the primitive endoderm—is involved in specifying neural fatein the mouse (Bouwmeester et al., BioEssays 19:855, 1997; reviewed inDavidson et al., “Cell lineage and Fate Determination”, Academic Press,1999; pp. 491-504 at 498). Endoderm ablation experiments stronglyimplicate an interaction of two germ layers that successively expressthe Hesx1 gene during gestation—which raises the possibility that suchinteractions may be critical for the specification of neural fate of theepiblast. Chimeric embryos deficient in the nodal gene fail to developforebrain (Varlet et al., Development 124:1033, 1997). Results of nodaland hex1 studies strongly suggest that there is a critical requirementfor the specification of neural cells in the epiblast. In addition,isolated epiblast from early embryos is unable to express brain specificgenes Otx2, En1, and En2 unless they are cultured together withfragments of the mesoendoderm. This evidence suggests that cells fromall three germ layers participate in neural differentiation in theepiblast.

Cells from all three germ layers are present in embryoid bodies, andprovide an amalgam of signaling that may be similar to signaling thatoccurs during normal embryo development. But this type of interactionbetween different cell types is lacking when pPS cells are plated inmonolayers.

Contrary to previous expectations, it has now been discovered thatplating undifferentiated hES cells directly onto a suitable surface orchanging medium in monolayer culture provides a system whereby adifferentiated cell population may be reliably derived—in spite of thesignaling one might expect to be lacking from cells of other germlayers.

In an exemplary experiment, cultures of rhesus and human ES lines grownon feeder cells were harvested using collagenase, and the cells werethen dissociated to clusters of ˜50-100 cells. The cells were thenplated onto glass coverslips coated with poly-ornithine, and culturedfor 1 week. Cultures showed positive immunoreactivity for β-tubulin IIIand MAP-2, markers that are characteristic of neurons; glial fibrillaryacidic protein (GFAP), which is characteristic of astrocytes; and GalC,which is characteristic of oligodendrocytes—indicating that all threemajor cell phenotypes of the central nervous system were present.

Under optimized conditions, this system can provide a remarkablyconsistent population of differentiated cells, with less heterogeneitythan what is present in a population of embryoid-body derived cells.Example 5 of this disclosure illustrates that the direct differentiationmethod can be used to obtain populations that are highly enriched fordopaminergic neurons. The direct differentiation method provides animportant source of reproducible high-quality cells for use in therapyand drug screening.

DEFINITIONS

Prototype “primate Pluripotent Stem cells” (pPS cells) are pluripotentcells derived from pre-embryonic, embryonic, or fetal tissue at any timeafter fertilization, and have the characteristic of being capable underthe right conditions of producing progeny of several different celltypes. pPS cells are capable of producing progeny that are derivativesof each of the three germinal layers: endoderm, mesoderm, and ectoderm,according to a standard art-accepted test, such as the ability to form ateratoma in a suitable host.

Included in the definition of pPS cells are embryonic cells of varioustypes, exemplified by human embryonic stem (hES) cells, as described byThomson et al. (Science 282:1145, 1998); embryonic stem cells from otherprimates, such as Rhesus or marmoset stem cells described by Thomson etal. (Proc. Natl. Acad. Sci. USA 92:7844, 1995; Developmental Biology38:133, 1998); and human embryonic germ (hEG) cells, described inShamblott et al. (Proc. Natl. Acad. Sci. USA 95:13726, 1998). Othertypes of pluripotent cells are also included in the term. Any cells ofprimate origin that are capable of producing progeny that arederivatives of all three germinal layers are included, regardless ofwhether they were derived from embryonic tissue, fetal tissue, or othersources. For many embodiments of the invention, it is beneficial to usepPS cells that are karyotypically normal and not derived from amalignant source.

pPS cell cultures are described as “undifferentiated” or “substantiallyundifferentiated” when a substantial proportion of stem cells and theirderivatives in the population display morphological characteristics ofundifferentiated cells, clearly distinguishing them from differentiatedcells of embryo or adult origin. Undifferentiated pPS cells are easilyrecognized by those skilled in the art, and typically appear in the twodimensions of a microscopic view with high nuclear/cytoplasmic ratiosand prominent nucleoli. It is understood that colonies ofundifferentiated cells within the population will often be surrounded byneighboring cells that are differentiated. Nevertheless, theundifferentiated colonies persist when the population is cultured orpassaged under appropriate conditions, and individual undifferentiatedcells constitute a substantial proportion of the cell population.Cultures that are substantially undifferentiated contain at least 20%undifferentiated pPS cells, and may contain at least 40%, 60%, or 80% inorder of increasing preference (in terms percentage of cells with thesame genotype that are undifferentiated). Using the methods described inthis disclosure, it is sometimes possible to develop or passage culturesthat contain a relatively low proportion of differentiated pPS cells(even as low as 5 or 10%) into cultures that are substantiallyundifferentiated.

Whenever a culture or cell population is referred to in this disclosureas proliferating “without differentiation”, what is meant is that afterproliferation, the composition is substantially undifferentiatedaccording to the preceding definition. Populations that proliferatethrough at least four passages (˜20 doublings) without differentiationwill contain substantially the same proportion of undifferentiated cells(or possibly a higher proportion of undifferentiated cells) whenevaluated at the same degree of confluence as the originating culture.

“Feeder cells” or “feeders” are cells of one type that are co-culturedwith cells of another type, to provide an environment in which the cellsof the second type can grow. The feeder cells are optionally from adifferent species as the cells they are supporting. For example, certaintypes of pPS cells can be supported by primary cultures of mouseembryonic fibroblasts, immortalized mouse embryonic fibroblasts, orhuman fibroblast-like cells differentiated from hES cells, as describedlater in this disclosure. In coculture with pPS cells, feeder cells aretypically inactivated by irradiation or treatment with an anti-mitoticagent such as mitomycin c, to prevent them from outgrowing the cellsthey are supporting. For use in producing conditioned medium,inactivation of the cells may be optional, and depends in part onmechanical aspects of medium production.

pPS cell populations are said to be “essentially free” of feeder cellsif the cells have been grown through at least one round after splittingin which fresh feeder cells are not added to support the growth of thepPS. It is recognized that if a previous culture containing feeder cellsis used as a source of pPS for the culture to which fresh feeders arenot added, there will be some feeder cells that survive the passage. Forexample, hES cells are often cultured in a 9.6 cm² well on a surface of˜375,000 primary irradiated embryonic fibroblasts near confluence. Bythe end of the culture, perhaps 150,000 feeder cells are still viable,and will be split and passaged along with hES that have proliferated toa number of ˜1 to 1.5 million. After a 1:6 split, the hES cellsgenerally resume proliferation, but the fibroblasts will not grow andonly a small proportion will be viable by the end of ˜6 days of culture.This culture is essentially free of feeder cells, with compositionscontaining less than about 5% feeder cells. Compositions containing lessthan 1%, 0.2%, 0.05%, or 0.01% feeder cells (expressed as % of totalcells in the culture) are increasingly more preferred.

Whenever a culture or cell population is referred to in this disclosureas “feeder-free”, what is meant is that the composition is essentiallyfree of feeder cells according to the preceding definition, subject onlyto further constraints if explicitly required.

A “growth environment” is an environment in which cells of interest willproliferate or differentiate in vitro. Features of the environmentinclude the medium in which the cells are cultured, the temperature, thepartial pressure of O₂ and CO₂, and a supporting structure (such as asubstrate on a solid surface) if present.

A “nutrient medium” is a medium for culturing cells containing nutrientsthat promote proliferation. The nutrient medium may contain any of thefollowing in an appropriate combination: isotonic saline, buffer, aminoacids, antibiotics, serum or serum replacement, and exogenously addedfactors. A “conditioned medium” is prepared by culturing a firstpopulation of cells in a medium, and then harvesting the medium. Theconditioned medium (along with anything secreted into the medium by thecells) may then be used to support the growth of a second population ofcells.

“Embryoid bodies” is a term of art synonymous with “aggregate bodies”.The terms refer to aggregates of differentiated and undifferentiatedcells that appear when pPS cells overgrow in plated or suspensioncultures.

“Restricted developmental lineage cells” are cells derived fromembryonic tissue, typically by differentiation or partialdifferentiation of pPS cells. These cells are capable of proliferatingand differentiating into several different cell types, but the range oftheir repertory is restricted. Examples are hematopoietic cells, whichare pluripotent for blood cell types, and hepatocyte progenitors, whichare pluripotent for sinusoidal endothelial cells, hepatocytes, andpotentially other liver cells. Another example is neural restrictedcells, which can generate glial cell precursors that progress tooligodendrocytes and astrocytes, and neuronal precursors that progressto neurons.

A cell is said to be “genetically altered”, “transfected”, or“genetically transformed” when a polynucleotide has been transferredinto the cell by any suitable means of artificial manipulation, or wherethe cell is a progeny of the originally altered cell that has inheritedthe polynucleotide. The polynucleotide will often comprise atranscribable sequence encoding a protein of interest, which enables thecell to express the protein at an elevated level. Also included aregenetic alterations by any means that result in functionally altering orabolishing the action of an endogenous gene. The genetic alteration issaid to be “inheritable” if progeny of the altered cell has the samealteration.

A “cell line” is a population of cells that can be propagated in culturethrough at least 10 passages. The population can be phenotypicallyhomogeneous, or the population can be a mixture of measurably differentphenotypes. Characteristics of the cell line are those characteristicsof the population as a whole that are essentially unaltered after 10passages.

A cell is described as “telomerized” if it has been genetically alteredwith a nucleic acid encoding a telomerase reverse transcriptase (TERT)of any species in such a manner that the TERT is transcribed andtranslated in the cell. The term also applies to progeny of theoriginally altered cell that have inherited the ability to express theTERT encoding region at an elevated level. The TERT encoding sequence istypically taken or adapted from a mammalian TERT gene, exemplified byhuman and mouse TERT, as indicated below.

A cell line is described as “permanent” or “immortalized” if it has atleast one of the following properties: 1) it has been geneticallyaltered for elevated expression of telomerase reverse transcriptase(TERT), detectable, for example, as increased telomerase activity inTRAP assay; 2) for cell lines otherwise capable of no more than 15population doublings, it has been genetically altered to extend itsreplicative capacity under suitable culture conditions to at least 20population doublings; or 3) for cell lines otherwise capable of morethan 15 population doublings, it has been genetically altered tosignificantly extend the replicative capacity of the cell line undertypical culture conditions. It is understood that cells meeting thisdefinition include not only the original genetically altered cells, butalso all progeny of such cells that meet the listed criteria.

The term “antibody” as used in this disclosure refers to both polyclonaland monoclonal antibody. The ambit of the term deliberately encompassesnot only intact immunoglobulin molecules, but also fragments andderivatives of immunoglobulin molecules (such as single chain Fvconstructs), and fragments and derivatives of immunoglobulin equivalentssuch as T-cell receptors, as may be prepared by techniques known in theart, and retaining the desired antigen binding specificity.

General Techniques

For further elaboration of general techniques useful in the practice ofthis invention, the practitioner can refer to standard textbooks andreviews in cell biology, tissue culture, and embryology. Included areTeratocarcinomas and embryonic stem cells: A practical approach (E. J.Robertson, ed., IRL Press Ltd. 1987); Guide to Techniques in MouseDevelopment (P. M. Wasserman et al., eds., Academic Press 1993);Embryonic Stem Cell Differentiation in Vitro (M. V. Wiles, Meth.Enzymol. 225:900, 1993); Properties and uses of Embryonic Stem Cells:Prospects for Application to Human Biology and Gene Therapy (P. D.Rathjen et al., al., 1993). Differentiation of stem cells is reviewed inRobertson, Meth. Cell Biol. 75:173, 1997; and Pedersen, Reprod. Fertil.Dev. 10:31, 1998.

Methods in molecular genetics and genetic engineering are describedgenerally in the current editions of Molecular Cloning: A LaboratoryManual, (Sambrook et al.); Oligonucleotide Synthesis (M. J. Gait, ed.);Animal Cell Culture (R. I. Freshney, ed.); Gene Transfer Vectors forMammalian Cells (Miller & Calos, eds.); Current Protocols in MolecularBiology and Short Protocols in Molecular Biology, 3rd Edition (F. M.Ausubel et al., eds.); and Recombinant DNA Methodology (R. Wu ed.,Academic Press). Reagents, cloning vectors, and kits for geneticmanipulation referred to in this disclosure are available fromcommercial vendors such as BioRad, Stratagene, Invitrogen, and ClonTech.

For general techniques involved in preparation of mRNA and cDNAlibraries and their analysis, those skilled in the art have access toRNA Methodologies: A Laboratory Guide for Isolation and Characterization(R. E. Farrell, Academic Press, 1998); cDNA Library Protocols (Cowell &Austin, eds., Humana Press); Functional Genomics (Hunt & Livesey, eds.,2000); and the Annual Review of Genomics and Human Genetics (E Lander,ed., published yearly by Annual Reviews). General techniques used inraising, purifying and modifying antibodies, and the design andexecution of immunoassays including immunocytochemistry, the reader isreferred to Handbook of Experimental Immunology (Weir & Blackwell,eds.); Current Protocols in Immunology (Coligan et al., eds.); andMethods of Immunological Analysis (Masseyeff et al., eds., Weinheim: VCHVerlags GmbH).

General techniques in cell culture and media collection are outlined inLarge Scale Mammalian Cell Culture (Hu et al., Curr. Opin. Biotechnol.8:148, 1997); Serum-free Media (K. Kitano, Biotechnology 17:73, 1991);Large Scale Mammalian Cell Culture (Curr. Opin. Biotechnol. 2:375,1991); and Suspension Culture of Mammalian Cells (Birch et al.,Bioprocess Technol. 19:251, 1990).

Sources of Pluripotent Stem Cells

Suitable source cells for culturing and differentiation according tothis invention include established lines of pluripotent cells derivedfrom tissue formed after gestation. Exemplary primary tissue sources areembryonic tissue (such as a blastocyst), or fetal tissue taken any timeduring gestation, typically but not necessarily before 10 weeksgestation. Non-limiting exemplars are established lines of primateembryonic stem (ES) and embryonic germ (EG) cells. Also contemplated isuse of the techniques of this disclosure during the initialestablishment or stabilization of such cells, in which case the sourcecells would be primary pluripotent cells taken directly from the tissueslisted.

Media and Feeder Cells

Media for isolating and propagating pPS cells can have any of severaldifferent formulas, as long as the cells obtained have the desiredcharacteristics, and can be propagated further. Suitable sources are asfollows: Dulbecco's modified Eagles medium (DMEM), Gibco # 11965-092;Knockout Dulbecco's modified Eagles medium (KO DMEM), Gibco # 10829-018;200 mM L-glutamine, Gibco # 15039-027; non-essential amino acidsolution, Gibco 11140-050; β-mercaptoethanol, Sigma # M7522; humanrecombinant basic fibroblast growth factor (bFGF), Gibco # 13256-029.Exemplary serum-containing ES medium is made with 80% DMEM (typically KODMEM), 20% defined fetal bovine serum (FBS) not heat inactivated, 0.1 mMnon-essential amino acids, 1 mM L-glutamine, and 0.1 mMβ-mercaptoethanol. The medium is filtered and stored at 4° C. Serum-freeES medium is made with 80% KO DMEM, 20% serum replacement, 0.1 mMnon-essential amino acids, 1 mM L-glutamine, and 0.1 mMβ-mercaptoethanol. Not all serum replacements work; an effective serumreplacement is Gibco # 10828-028 (proprietary formula; productobtainable from the manufacturer). The medium is filtered and stored at4° C. Just before use, human bFGF is added to a final concentration of 4ng/mL.

pPS cells are typically cultured on a layer of feeder cells that supportthe pPS cells in various ways, such as the production of soluble factorsthat promote pPS cell survival or proliferation, or inhibitdifferentiation. Feeder cells are typically fibroblast type cells, oftenderived from embryonic or fetal tissue. A frequently used source ismouse embryo. Useful feeder cell lines have been obtained by obtainingembryonic fibroblasts, transfecting them to express telomerase, and thenpassaging them or freezing them for future use. The cell lines areplated to near confluence, irradiated to prevent proliferation, and usedto support pPS cell cultures.

In one illustration, pPS cells are first derived and supported onprimary embryonic fibroblasts. Mouse embryonic fibroblasts (mEF) can beobtained from outbred CF1 mice (SASCO) or other suitable strains. Theabdomen of a mouse at 13 days of pregnancy is swabbed with 70% ethanol,and the decidua is removed into phosphate buffered saline (PBS). Embryosare harvested; placenta, membranes, and soft tissues are removed; andthe carcasses are washed twice in PBS. They are then transferred tofresh 10 cm bacterial dishes containing 2 mL trypsin/EDTA, and finelyminced. After incubating 5 min at 37° C., the trypsin is inactivatedwith 5 mL DMEM containing 10% FBS, and the mixture is transferred to a15 mL conical tube. Debris is allowed to settle for 2 min, thesupernatant is made up to a final volume of 10 mL, and plated onto a 10cm tissue culture plate or T75 flask. The flask is incubated undisturbedfor 24 h, after which the medium is replaced. When flasks are confluent(˜2-3 d), they are split 1:2 into new flasks.

Feeder cells are propagated in mEF medium, containing 90% DMEM (Gibco #11965-092), 10% FBS (Hyclone # 30071-03), and 2 mM glutamine. mEFs arepropagated in T150 flasks (Corning # 430825), splitting the cells 1:2every other day with trypsin, keeping the cells subconfluent. To preparethe feeder cell layer, cells are irradiated at a dose to inhibitproliferation but permit synthesis of important factors that support hEScells (˜4000 rads gamma irradiation). Six-well culture plates (such asFalcon # 304) are coated by incubation at 37° C. with 1 mL 0.5% gelatinper well overnight, and plated with ˜375,000 irradiated mEFs per well.Feeder cell layers are used 5 h to 4 days after plating. The medium isreplaced with fresh hES medium just before seeding pPS cells.

Preparation of Human Embryonic Stem (hES) Cells

Human embryonic stem (hES) cells can be prepared as described by Thomsonet al. (U.S. Pat. No. 5,843,780; Science 282:1145, 1998; Curr. Top. Dev.Biol. 38:133 ff., 1998; Proc. Natl. Acad. Sci. USA 92:7844, 1995).

Briefly, human blastocysts are obtained from human in vivopreimplantation embryos. Alternatively, in vitro fertilized (IVF)embryos can be used, or one cell human embryos can be expanded to theblastocyst stage (Bongso et al., Hum Reprod 4: 706, 1989). Human embryosare cultured to the blastocyst stage in G1.2 and G2.2 medium (Gardner etal., Fertil. Steril. 69:84, 1998). Blastocysts that develop are selectedfor ES cell isolation. The zona pellucida is removed from blastocysts bybrief exposure to pronase (Sigma). The inner cell masses are isolated byimmunosurgery, in which blastocysts are exposed to a 1:50 dilution ofrabbit anti-human spleen cell antiserum for 30 minutes, then washed for5 minutes three times in DMEM, and exposed to a 1:5 dilution of Guineapig complement (Gibco) for 3 min (see Solter et al., Proc. Natl. Acad.Sci. USA 72:5099, 1975). After two further washes in DMEM, lysedtrophectoderm cells are removed from the intact inner cell mass (ICM) bygentle pipetting, and the ICM plated on mEF feeder layers.

After 9 to 15 days, inner cell mass-derived outgrowths are dissociatedinto clumps either by exposure to calcium and magnesium-freephosphate-buffered saline (PBS) with 1 mM EDTA, by exposure to dispaseor trypsin, or by mechanical dissociation with a micropipette; and thenreplated on mEF in fresh medium. Dissociated cells are replated on mEFfeeder layers in fresh ES medium, and observed for colony formation.Colonies demonstrating undifferentiated morphology are individuallyselected by micropipette, mechanically dissociated into clumps, andreplated. ES-like morphology is characterized as compact colonies withapparently high nucleus to cytoplasm ratio and prominent nucleoli.Resulting ES cells are then routinely split every 1-2 weeks by brieftrypsinization, exposure to Dulbecco's PBS (without calcium or magnesiumand with 2 mM EDTA), exposure to type IV collagenase (˜200 U/mL; Gibco)or by selection of individual colonies by micropipette. Clump sizes ofabout 50 to 100 cells are optimal.

Preparation of Human Embryonic Germ (hEG) Cells

Human Embryonic Germ (hEG) cells can be prepared from primordial germcells present in human fetal material taken about 8-11 weeks after thelast menstrual period. Suitable preparation methods are described inShamblott et al., Proc. Natl. Acad. Sci. USA 95:13726, 1998 and U.S.Pat. No. 6,090,622.

Briefly, genital ridges are rinsed with isotonic buffer, then placedinto 0.1 mL 0.05% trypsin/0.53 mM sodium EDTA solution (BRL) and cutinto <1 mm³ chunks. The tissue is then pipetted through a 100 μL tip tofurther disaggregate the cells. It is incubated at 37° C. for ˜5 min,then ˜3.5 mL EG growth medium is added. EG growth medium is DMEM, 4500mg/L D-glucose, 2200 mg/L mM sodium bicarbonate; 15% ES qualified fetalcalf serum (BRL); 2 mM glutamine (BRL); 1 mM sodium pyruvate (BRL);1000-2000 U/mL human recombinant leukemia inhibitory factor (LIF,Genzyme); 1-2 ng/ml human recombinant basic fibroblast growth factor(bFGF, Genzyme); and 10 μM forskolin (in 10% DMSO). In an alternativeapproach, EG cells are isolated using hyaluronidase/collagenase/DNAse.Gonadal anlagen or genital ridges with mesenteries are dissected fromfetal material, the genital ridges are rinsed in PBS, then placed in 0.1ml HCD digestion solution (0.01% hyaluronidase type V, 0.002% DNAse I,0.1% collagenase type IV, all from Sigma prepared in EG growth medium).Tissue is minced and incubated 1 h or overnight at 37° C., resuspendedin 1-3 mL of EG growth medium, and plated onto a feeder layer.

Ninety-six well tissue culture plates are prepared with a sub-confluentlayer of feeder cells cultured for 3 days in modified EG growth mediumfree of LIF, bFGF or forskolin, inactivated with 5000 rad γ-irradiation.Suitable feeders are STO cells (ATCC Accession No. CRL 1503). ˜0.2 mL ofprimary germ cell (PGC) suspension is added to each of the wells. Thefirst passage is conducted after 7-10 days in EG growth medium,transferring each well to one well of a 24-well culture dish previouslyprepared with irradiated STO mouse fibroblasts. The cells are culturedwith daily replacement of medium until cell morphology consistent withEG cells are observed, typically after 7-30 days or 1-4 passages.

Propagation of pPS Cells

pPS cells can be propagated continuously in culture, using a combinationof culture conditions that support proliferation without promotingdifferentiation. It has been determined that hES cells can be grownwithout differentiation, even in the absence of feeder cells. Forfeeder-free culture, it is beneficial to provide a compatible culturesurface (the substrate), and a nutrient medium that supplies some of theinfluences provided by the feeder cells.

Particularly suitable as a substrate for feeder-free pPS culture areextracellular matrix components (derived from basement membrane, orforming part of adhesion molecule receptor-ligand couplings). Acommercial preparation is available from Becton Dickenson under the nameMatrigel®, and can be obtained in regular or Growth Factor Reducedformulation. Both formulations are effective. Matrigel® is a solublepreparation from Engelbreth-Holm-Swarm tumor cells that gels at roomtemperature to form a reconstituted basement membrane.

Other extracellular matrix components and component mixtures aresuitable as an alternative. Depending on the cell type beingproliferated, this may include laminin, fibronectin, proteoglycan,entactin, heparan sulfate, and the like, alone or in variouscombinations. Laminins are major components of all basal laminae invertebrates, which interact with integrin heterodimers such as α6β1 andα6β4 (specific for laminins) and other heterodimers (that cross-reactwith other matrices). Using culture conditions illustrated in theexamples, collagen IV supports hES cell growth, while collagen I doesnot. Substrates that can be tested using the experimental proceduresdescribed herein include not only other extracellular matrix components,but also polyamines (such as poly-ornithine, poly-lysine), and othercommercially available coatings.

The pluripotent cells are plated onto the substrate in a suitabledistribution and in the presence of a medium that promotes cellsurvival, propagation, and retention of the desirable characteristics.These characteristics benefit from careful attention to the seedingdistribution. One feature of the distribution is the plating density. Ithas been found that plating densities of at least ˜15,000 cells cm⁻²promote survival and limit differentiation. Typically, a plating densityof between about 90,000 cm⁻² and about 170,000 cm⁻² is used.

Another feature is the dispersion of cells. The propagation of mousestem cells involves dispersing the cells into a single-cell suspension(Robinson, Meth. Mol. Biol. 75:173, 1997 at page 177). In contrast,passaging primate PS cells has previously thought to require keeping thecells together in small clusters. Enzymatic digestion is halted beforecells become completely dispersed (say, ˜5 min with collagenase IV). Theplate is then scraped gently with a pipette, and the cells aretriturated with the pipette until they are suspended as clumps ofadherent cells, about 10-2000 cells in size. The clumps are then plateddirectly onto the substrate without further dispersal.

It has been discovered that primate PS cells can be passaged betweenfeeder-free cultures as a finer cell suspension, providing that anappropriate enzyme and medium are chosen, and the plating density issufficiently high. By way of illustration, confluent human embryonicstem cells cultured in the absence of feeders are removed from theplates by incubating with a solution of 0.05% (wt/vol) trypsin (Gibco)and 0.053 mM EDTA for 5-15 min at 37° C. With the use of pipette, theremaining cells in the plate are removed and the cells are trituratedwith the pipette until the cells are dispersed into a suspensioncomprising single cells and some small clusters. The cells are thenplated at densities of 50,000-200,000 cells/cm² to promote survival andlimit differentiation. The phenotype of ES cells passaged by thistechnique is similar to what is observed when cells are harvested asclusters by collagen digestion. As another option, the cells can beharvested without enzymes before the plate reaches confluence. The cellsare incubated ˜5 min in a solution of 0.5 mM EDTA alone in PBS, washedfrom the culture vessel, and then plated into a new culture withoutfurther dispersal.

pPS cells plated in the absence of fresh feeder cells benefit from beingcultured in a nutrient medium. The medium will generally contain theusual components to enhance cell survival, including isotonic buffer,essential minerals, and either serum or a serum replacement of somekind. Particularly beneficial is a medium that has been conditioned tosupply some of the elements otherwise provided by feeder cells.

Feeder cells typically contain fibroblast type cells. Primary embryonicor fetal feeder cell cultures are a mixed population of cells,containing cells that have morphology of fibroblasts and of early muscleand neuronal cells. Different cells in the population may play differentroles in supporting pPS culture, and the distribution and character ofthe culture may change.

As an alternative to primary mouse fibroblast cultures, conditionedmedium can be prepared from other cell types, such as established celllines. More permanent feeder cell lines can be developed for producingmedium according to this invention using embryonic fibroblasts from anon-human species such as a mouse, genetically altered with animmortalizing gene, such as a gene that expresses telomerase.

It has also been discovered that cells with particular characteristicsdifferentiated from human embryo derived cells can be used to supportculture of undifferentiated pPS cells. Certain fibroblast-like cells ormesenchymal cells derived from human embryo cells have this property,and can be identified according to the assay described earlier. Anexemplary method for obtaining suitable cells involves differentiating aculture of pPS cells (such as hES cells). Differentiated cells with aparticular phenotype are selected from amongst the mixed differentiatedcell population, and medium conditioned by culturing with the selectedcells is tested for its ability to support growth of pPS cells in aculture environment essentially free of feeder cells. As illustrated inthe examples below, medium that has been conditioned for 1-2 days istypically used to support pPS cell culture for 1-2 days, and thenexchanged. Conditioned medium is used to support pPS cells undiluted, ortitrated to an effective level of dilution. The conditioned medium canbe supplemented before use with additional growth factors that benefitpPS cell culture. It is often beneficial to add growth factors such asbFGF or FGF-4 to the medium both before conditioning, and then againbefore using the medium to support the growth of pPS cells.

It should be recognized that each of the conditions described here canbe optimized independently, and certain combinations of conditions willprove effective upon further testing. Such optimization is a matter ofroutine experimentation, and does not depart from the spirit of theinvention provided in this disclosure.

Characteristics of pPS Cells

Human ES cells have the characteristic morphological features ofundifferentiated stem cells. In the two dimensions of a standardmicroscopic image, hES cells have high nuclear/cytoplasmic ratios in theplane of the image, prominent nucleoli, and compact colony formationwith poorly discernable cell junctions. Cell lines can be karyotypedusing a standard G-banding technique (available at many clinicaldiagnostics labs that provides routine karyotyping services, such as theCytogenetics Lab at Oakland Calif.) and compared to published humankaryotypes. It is desirable to obtain cells that have a “normalkaryotype”, which means that the cells are euploid, wherein all humanchromosomes are present and are not noticeably altered.

hES and hEG cells can also be characterized by expressed cell markers.In general, the tissue-specific markers discussed in this disclosure canbe detected using a suitable immunological technique—such as flowcytometry for membrane-bound markers, immunocytochemistry forintracellular markers, and enzyme-linked immunoassay, for markerssecreted into the medium. The expression of protein markers can also bedetected at the mRNA level by reverse transcriptase-PCR usingmarker-specific primers. See U.S. Pat. No. 5,843,780 for furtherdetails.

Stage-specific embryonic antigens (SSEA) are characteristic of certainembryonic cell types. Antibodies for SSEA-1, SSEA-3 and SSEA-4 areavailable from the Developmental Studies Hybridoma Bank of the NationalInstitute of Child Health and Human Development (Bethesda Md.). Otheruseful markers are detectable using antibodies designated Tra-1-60 andTra-1-81 (Andrews et al., Cell Lines from Human Germ Cell Tumors, in E.J. Robertson, 1987, supra). Mouse ES cells can be used as a positivecontrol for SSEA-1, and as a negative control for SSEA-4, Tra-1-60, andTra-1-81. SSEA-4 is consistently present on human embryonal carcinoma(hEC) cells. Differentiation of pPS cells in vitro results in the lossof SSEA-4, Tra-1-60, and Tra-1-81 expression and increased expression ofSSEA-1. SSEA-1 is also found on hEG cells. pPS cells can also becharacterized by the presence of alkaline phosphatase activity, whichcan be detected by fixing the cells with 4% paraformaldehyde, and thendeveloping with Vector Red as a substrate, as described by themanufacturer (Vector Laboratories, Burlingame Calif.). Expression ofhTERT and OCT-4 (detectable by RT-PCR) and telomerase activity(detectable by TRAP assay) are also characteristic of many types ofundifferentiated pPS cells.

Where it is desirable to increase the replicative capacity of pPS cells,or cells differentiated from them, they can be immortalized ortelomerized (either before or after differentiation) using the methodsdescribed below.

Differentiation of Propagated pPS Cells

This invention provides a new system for differentiating pPS cells intocommitted precursor cells or fully differentiated cells without formingembryoid bodies as an intermediate step.

Culturing embryoid bodies according to traditional methods are reportedin O'Shea, Anat. Rec. (New Anat. 257:323, 1999). pPS cells are culturedin a manner that permits aggregates to form, for which many options areavailable: for example, by overgrowth of a donor pPS cell culture, or byculturing pPS cells in suspension in culture vessels having a substratewith low adhesion properties which allows EB formation. pPS cells areharvested by brief collagenase digestion, dissociated into clusters, andplated in non-adherent cell culture plates. The aggregates are fed everyfew days, and then harvested after a suitable period, typically 4-8days.

The cells can then be cultured in a medium and/or on a substrate thatpromotes enrichment of cells of a particular lineage. The substrate cancomprise matrix components such as Matrigel® (Becton Dickenson),laminin, collagen, gelatin, or matrix produced by first culturing amatrix-producing cell line (such as a fibroblast or endothelial cellline), and then lysing and washing in such a way that the matrix remainsattached to the surface of the vessel. Embryoid bodies comprise aheterogeneous cell population, potentially having an endoderm exterior,and a mesoderm and ectoderm interior.

The Direct Differentiation Method

It has now been discovered that pPS cells can be differentiated intocommitted precursor cells or terminally differentiated cells withoutforming embryoid bodies or aggregates as an intermediate step.

Briefly, a suspension of undifferentiated pPS cells is prepared, andthen plated onto a solid surface that promotes differentiation. Ingeneral, cultures of pPS cells are typically harvested when they haveproliferated to an adequate density, but not to the point ofover-confluence, because the cells will differentiate in an uncontrolledfashion if allowed to overgrow. A suitable suspension can be prepared byincubating the culture dish with Collagenase IV for about 5-20 min, andthen scraping the cells from the dish. The cells can be dissociated, forexample, by triturating in a pipette. For many types of differentiation,it is recommended that the cells not be completely dissociated, so thatthe majority of pPS is in clumps of about 10 to 200 cells.

The suspension is then plated onto a substrate that promotes regulateddifferentiation into committed precursor cells. Suitable substratesinclude glass or plastic surfaces that are adherent. For example, glasscoverslips can be coated with a poly-cationic substance, such as apolyamine like poly-lysine, poly-ornithine, or other homogeneous ormixed polypeptides or other polymers with a predominant positive charge.The cells are then cultured in a suitable nutrient medium that isadapted to promote differentiation towards the desired cell lineage.

In some instances, differentiation is promoted by withdrawing serum orserum replacement from the culture medium. This can be achieved bysubstituting a medium devoid of serum and serum replacement, forexample, at the time of replating, by withdrawing one or more componentsof the medium that promotes growth of undifferentiated cells or inhibitsdifferentiation. Examples include certain growth factors, mitogens,leukemia inhibitory factor (LIF), fibroblast growth factors such asbFGF, and other components in conditioned medium. The new medium is saidto be “essentially free” of these components when it contains <5% andpreferably <1% of the usual concentration of the component used inculturing the cells in an undifferentiated form.

In some instances, differentiation is promoted by adding a mediumcomponent that promotes differentiation towards the desired celllineage, or inhibits the growth of cells with undesired characteristics.For example, to generate cells committed to neural or glial lineages,the medium can include any of the following factors or mediumconstituents in an effective combination: Brain derived neurotrophicfactor (BDNF), neutrotrophin-3 (NT-3), NT-4, epidermal growth factor(EGF), ciliary neurotrophic factor (CNTF), nerve growth factor (NGF),retinoic acid (RA), sonic hedgehog, FGF-8, ascorbic acid, forskolin,fetal bovine serum (FBS), and bone morphogenic proteins (BMPs). Otherexemplary factors are listed in Example 5.

Under appropriate conditions, the direct differentiation method providesa cell population that is less heterogeneous than what is typicallyfound in embryoid body derived cells. Unless explicitly indicatedotherwise, the method can include a small degree of overgrowth,aggregate formation, or formation of occasional embryoid body-likestructure—however, this is a collateral occurrence, and not required fordifferentiation of the cells into the committed precursor or terminallydifferentiated cell population desired. Typically, less than ˜10% of thedifferentiated cell population will be progeny of cells that grew out ofembryoid bodies, with levels of less than ˜3% or 1% being achievable incertain circumstances.

General principals for obtaining tissue cells from pluripotent stemcells are reviewed in Pedersen (Reprod. Fertil. Dev. 6:543, 1994), andU.S. Pat. No. 6,090,622. For neural progenitors, neural restrictivecells and glial cell precursors, see Bain et al., Biochem. Biophys. Res.Commun. 200:1252, 1994; Trojanowski et al., Exp. Neurol. 144:92, 1997;Wojcik et al., Proc. Natl. Acad. Sci. USA 90:1305-130; Mujtaba et al.,Dev. Biol. 214:113, 1999; and U.S. Pat. Nos. 5,851,832, 5,928,947,5,766,948, and 5,849,553. For cardiac muscle and cardiomyocytes see Chenet al., Dev. Dynamics 197:217, 1993 and Wobus et al., Differentiation48:173, 1991. For hematopoietic progenitors, see Burkert et al., NewBiol. 3:698, 1991 and Biesecker et al., Exp. Hematol. 21:774, 1993. U.S.Pat. No. 5,773,255 relates to glucose-responsive insulin secretingpancreatic beta cell lines. U.S. Pat. No. 5,789,246 relates tohepatocyte precursor cells. Other progenitors of interest include butare not limited to chondrocytes, osteoblasts, retinal pigment epithelialcells, fibroblasts, skin cells such as keratinocytes, dendritic cells,hair follicle cells, renal duct epithelial cells, smooth and skeletalmuscle cells, testicular progenitors, and vascular endothelial cells.

Scientists at Geron Corporation have discovered that culturing pPS cellsor embryoid body cells in the presence of ligands that bind growthfactor receptors promotes enrichment for neural precursor cells. Thegrowth environment may contain a neural cell supportive extracellularmatrix, such as fibronectin. Suitable growth factors include but are notlimited to EGF, bFGF, PDGF, IGF-1, and antibodies to receptors for theseligands. Cofactors such as retinoic acid may also be included. Thecultured cells may then be optionally separated based on whether theyexpress a marker such as A2B5. Under the appropriate circumstances,populations of cells enriched for expression of the A2B5 marker may havethe capacity to generate both neuronal cells (including mature neurons),and glial cells (including astrocytes and oligodendrocytes.

Optionally, the cell populations are further differentiated, forexample, by culturing in a medium containing an activator of cAMP.Factors useful in the direct differentiation method for producingneurons are explored in Example 5, below. Markers for identifying celltypes include β-tubulin III or microtubule-associated protein 2 (MAP-2),characteristic of neurons; glial fibrillary acidic protein (GFAP),present in astrocytes; galactocerebroside (GalC) or myelin basic protein(MBP); characteristic of oligodendrocytes; OCT-4, characteristic ofundifferentiated hES cells; Nestin or Musashi, characteristic of neuralprecursors and other cells; and both A2B5 and NCAM, which appear onpopulations of neural precursors differentiated from pPS cells.

Scientists at Geron Corporation have also discovered that culturing pPScells or embryoid body cells in the presence of a hepatocytedifferentiation agent promotes enrichment for hepatocyte-like cells. Thegrowth environment may contain a hepatocyte supportive extracellularmatrix, such as collagen or Matrigel®. Suitable differentiation agentsinclude various isomers of butyrate and their analogs, exemplified byn-butyrate. The cultured cells are optionally cultured simultaneously orsequentially with a hepatocyte maturation factor, such as an organicsolvent like dimethyl sulfoxide (DMSO); a maturation cofactor such asretinoic acid; or a cytokine or hormone such as a glucocorticoid,epidermal growth factor (EGF), insulin, transforming growth factors(TGF-α and TGF-β), fibroblast growth factors (FGF), heparin, hepatocytegrowth factors (HGF), interleukins (IL-1 and IL-6), insulin-like growthfactors (IGF-I and IGF-II), and heparin-binding growth factors (HBGF-1).

Characteristics of Differentiated Cells

Cells can be characterized according to a number of phenotypic criteria.The criteria include but are not limited to characterization ofmorphological features, detection or quantitation of expressed cellmarkers and enzymatic activity, and determination of the functionalproperties of the cells in vivo.

Markers of interest for neural cells include β-tubulin III orneurofilament, characteristic of neurons; glial fibrillary acidicprotein (GFAP), present in astrocytes; galactocerebroside (GalC) ormyelin basic protein (MBP); characteristic of oligodendrocytes; Oct-4,characteristic of undifferentiated hES cells; nestin, characteristic ofneural precursors and other cells. A2B5 and NCAM are characteristic ofglial progenitors and neural progenitors, respectively. Cells can alsobe tested for secretion of characteristic biologically activesubstances. For example, GABA-secreting neurons can be identified byproduction of glutamic acid decarboxylase or GABA. Dopaminergic neuronscan be identified by production of dopa decarboxylase, dopamine, ortyrosine hydroxylase.

Markers of interest for liver cells include α-fetoprotein (liverprogenitors); albumin, α₁-antitrypsin, glucose-6-phosphatase, cytochromep450 activity, transferrin, asialoglycoprotein receptor, and glycogenstorage (hepatocytes); CK7, CK19, and γ-glutamyl transferase (bileepithelium). It has been reported that hepatocyte differentiationrequires the transcription factor HNF-4α (Li et al., Genes Dev. 14:464,2000). Markers independent of HNF-4α expression include α₁-antitrypsin,α-fetoprotein, apoE, glucokinase, insulin growth factors 1 and 2, IGF-1receptor, insulin receptor, and leptin. Markers dependent on HNF-4αexpression include albumin, apoAI, apoAII, apoB, apoCIII, apoCII,aldolase B, phenylalanine hydroxylase, L-type fatty acid bindingprotein, transferrin, retinol binding protein, and erythropoietin (EPO).Hepatocyte lineage cells differentiated from pPS cells will typicallydisplay at least three of the following markers: α₁-antitrypsin (AAT)synthesis, albumin synthesis, asialoglycoprotein receptor (ASGR)expression, absence of α-fetoprotein, evidence of glycogen storage,evidence of cytochrome p450 activity, and evidence ofglucose-6-phosphatase activity.

Markers of interest for other cell types include the following. Forcardiomyocytes: GATA-4, Nkx2.5, cardiac troponin I, ANF, α-cardiacmyosin heavy chain (α-MHC), actin, or ventricular myosin light chain 2(MLC-2v). See Wobus et al., J. Mol. Cell. Cardiol. 29:1525, 1997. Forskeletal muscle: myoD, myogenin, and myf-5. For endothelial cells: PECAM(platelet endothelial cell adhesion molecule), Flk-1, tie-1, tie-2,vascular endothelial (VE) cadherin, MECA-32, and MEC-14.7. For smoothmuscle cells: specific myosin heavy chain. For pancreatic cells, pdx andinsulin secretion. For hematopoietic cells and their progenitors:GATA-1, CD34, β-major globulin, and μ-major globulin like gene PH1.

Certain tissue-specific markers listed in this disclosure or known inthe art can be detected by immunological techniques—such as flowimmunocytochemistry for cell-surface markers, immunohistochemistry (forexample, of fixed cells or tissue sections) for intracellular orcell-surface markers, Western blot analysis of cellular extracts, andenzyme-linked immunoassay, for cellular extracts or products secretedinto the medium. The expression of tissue-specific gene products canalso be detected at the mRNA level by Northern blot analysis, dot-blothybridization analysis, or by reverse transcriptase initiated polymerasechain reaction (RT-PCR) using sequence-specific primers in standardamplification methods. Sequence data for the particular markers listedin this disclosure can be obtained from public databases such as GenBank(URL www.ncbi.nim.nih.gov:80/entrez). Expression of tissue-specificmarkers as detected at the protein or mRNA level is considered positiveif the level is at least 2-fold, and preferably more than 10- or 50-foldabove that of a control cell, such as an undifferentiated pPS cell, afibroblast, or other unrelated cell type.

The system provided by this invention allows production of a relativelyuniform cell population, without the complexity of cells often obtainedby forming embryoid bodies. Cell populations derived by directdifferentiation may be 50%, 75%, 90%, or 98% homogeneous in terms ofmorphological characteristics of the desired cell type, or expression ofany of the markers indicated above. They may also be relatively devoidof undesired cell types, such as endothelial cells, mesenchymal cells,fibroblasts, smooth muscle cells, cells expressing α-myosin heavy chain,or other particular cell types of the endoderm, mesoderm, or ectoderm.

Modifying Differentiated Cells

Differentiated cells of this invention can be genetically altered in amanner that permits the genetic alteration to be either transient, orstable and inheritable as the cells divide. Undifferentiated cells canbe genetically altered and then differentiated into the desiredphenotype, or the cells can be differentiated first before geneticalteration.

Where the pPS cells are genetically altered before differentiation, thegenetic alteration can be performed on a permanent feeder cell line thathas resistance genes for drugs used to select for transformed cells, oron pPS cells grown in feeder-free culture.

Suitable methods for transferring vector plasmids into hES cells includelipid/DNA complexes, such as those described in U.S. Pat. Nos.5,578,475; 5,627,175; 5,705,308; 5,744,335; 5,976,567; 6,020,202; and6,051,429. Suitable reagents include lipofectamine, a 3:1 (w/w) liposomeformulation of the poly-cationic lipid2,3-dioleyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propanaminiumtrifluoroacetate (DOSPA) (Chemical Abstracts Registry name:N-[2-(2,5-bis[(3-aminopropyl)amino]-1-oxpentyl}amino)ethyl]-N,N-dimethyl-2,3-bis(9-octadecenyloxy)-1-propanaminiumtrifluoroacetate), and the neutral lipid dioleoylphosphatidylethanolamine (DOPE) in membrane filtered water. Exemplary isthe formulation Lipofectamine 2000™ (available from Gibco/LifeTechnologies # 11668019). Other reagents include: FuGENE™ 6 TransfectionReagent (a blend of lipids in non-liposomal form and other compounds in80% ethanol, obtainable from Roche Diagnostics Corp. # 1814443); andLipoTAXI™ transfection reagent (a lipid formulation from InvitrogenCorp., # 204110). Suitable viral vector systems for producing hES cellswith stable genetic alterations are based on adenovirus and retrovirus,and may be prepared using commercially available virus components.

For therapeutic use, it is usually desirable that differentiated cellpopulations be substantially free of undifferentiated pPS cells. One wayof depleting undifferentiated stem cells from the population is totransfect them with a vector in which an effector gene under control ofa promoter that causes preferential expression in undifferentiatedcells. Suitable promoters include the TERT promoter and the OCT-4promoter. The effector gene may be directly lytic to the cell (encoding,for example, a toxin or a mediator of apoptosis). Alternatively, theeffector gene may render the cell susceptible to toxic effects of anexternal agent, such as an antibody or a prodrug. Exemplary is a herpessimplex thymidine kinase (tk) gene, which causes cells in which it isexpressed to be susceptible to ganciclovir. Suitable TERT promoter tkconstructs are provided in WO 98/14593 (Morin et al.).

Increasing Replicative Capacity of Differentiated Cells

It is desirable that certain differentiated cells have the ability toreplicate in certain drug screening and therapeutic applications. Cellscan optionally be telomerized to increase their replication potential,either before or after they progress to restricted developmental lineagecells or terminally differentiated cells. pPS cells that are telomerizedmay be taken down the differentiation pathway described earlier; ordifferentiated cells can be telomerized directly.

Before and after telomerization, telomerase activity and expression ofhTERT gene product can be determined using commercially availablereagents and established methods. For example, pPS cells are evaluatedfor telomerase using TRAP activity assay (Kim et al., Science 266:2011,1997; Weinrich et al., Nature Genetics 17:498, 1997). Expression ofhTERT at the mRNA level is evaluated by RT-PCR.

Cells are telomerized by genetically altering them by transfection ortransduction with a suitable vector, homologous recombination, or otherappropriate technique, so that they express the telomerase catalyticcomponent (TERT). Particularly suitable is the catalytic component ofhuman telomerase (hTERT), provided in International Patent PublicationWO 98/14592. For certain applications, species homologs like mouse TERT(WO 99/27113) can also be used. Transfection and expression oftelomerase in human cells is described in Bodnar et al., Science279:349, 1998 and Jiang et al., Nat. Genet. 21:111, 1999. In anotherexample, hTERT clones (WO 98/14592) are used as a source of hTERTencoding sequence, and spliced into an EcoRI site of a PBBS212 vectorunder control of the MPSV promoter, or into the EcoRI site ofcommercially available pBABE retrovirus vector, under control of the LTRpromoter. Differentiated or undifferentiated pPS cells are geneticallyaltered using vector containing supernatants over a 8-16 h period, andthen exchanged into growth medium for 1-2 days. Genetically alteredcells are selected using 0.5-2.5 μg/mL puromycin, and recultured. Theycan then be assessed for hTERT expression by RT-PCR, telomerase activity(TRAP assay), immunocytochemical staining for hTERT, or replicativecapacity. Continuously replicating colonies will be enriched by furtherculturing under conditions that support proliferation, and cells withdesirable phenotypes can optionally be cloned by limiting dilution.

In certain embodiments of this invention, pPS cells are differentiated,and then genetically altered to express TERT. In other embodiments ofthis invention, pPS cells are genetically altered to express TERT, andthen differentiated. Successful modification to increase TERT expressioncan be determined by TRAP assay, or by determining whether thereplicative capacity of the cells has improved.

Other methods of immortalizing cells are also contemplated, such astransforming the cells with DNA encoding the SV40 large T antigen (U.S.Pat. No. 5,869,243, International Patent Publication WO 97/32972).Transfection with oncogenes or oncovirus products is less suitable whenthe cells are to be used for therapeutic purposes. Telomerized cells areof particular interest in applications of this invention where it isadvantageous to have cells that can proliferate and maintain theirkaryotype—for example, in pharmaceutical screening, and in therapeuticprotocols where differentiated or partially differentiated cells areadministered to an individual as part of a protocol to achieve tissueregeneration.

Use of Differentiated Cells

This description provides a method by which large numbers of pluripotentcells can be produced commercially, and then differentiated intocommitted precursor cells or terminally differentiated cells. These cellpopulations can be used for a number of important research, development,and commercial purposes.

Preparation of Expression Libraries and Specific Antibody

The differentiated cells of this invention can also be used to preparespecific antibody for phenotypic markers of differentiated cells.Polyclonal antibodies can be prepared by injecting a vertebrate animalwith cells of this invention in an immunogenic form. Production ofmonoclonal antibodies is described in such standard references as Harrow& Lane (1988), U.S. Pat. Nos. 4,491,632, 4,472,500 and 4,444,887, andMethods in Enzymology 73B:3 (1981). Other methods of obtaining specificantibody molecules (optimally in the form of single-chain variableregions) involve contacting a library of immunocompetent cells or viralparticles with the target antigen, and growing out positively selectedclones. See Marks et al., New Eng. J. Med. 335:730, 1996, InternationalPatent Publications WO 94/13804, WO 92/01047, WO 90/02809, and McGuinesset al., Nature Biotechnol. 14:1449, 1996.

By positively selecting using pPS of this invention, and negativelyselecting using cells bearing more broadly distributed antigens (such asdifferentiated embryonic cells) or adult-derived stem cells, the desiredspecificity can be obtained. The antibodies in turn can be used toidentify or rescue cells of a desired phenotype from a mixed cellpopulation, for purposes such as costaining during immunodiagnosis usingtissue samples, and isolating precursor cells from terminallydifferentiated cells, and cells of other lineages.

Differentiated pPS cells of this invention can also be used to preparemRNA and cDNA libraries that reflect the gene expression patterns ofthese cells. mRNA and cDNA can also be made from undifferentiated cells,and used to produce subtraction libraries enriched for transcripts thatare up- or down-regulated during differentiation. Further informationcan be found in U.S. patent application Ser. No. 09/688,031.

Screening Proliferation Factors, Differentiation Factors, andPharmaceuticals

pPS cells can be used to screen for factors (such as small moleculedrugs, peptides, polynucleotides, and the like) or conditions (such asculture conditions or manipulation) that affect the characteristics ofpPS cells in culture. This system has the advantage of not beingcomplicated by a secondary effect caused by perturbation of the feedercells by the test compound. In one application, growth affectingsubstances are tested. The conditioned medium is withdrawn from theculture and a simpler medium (such as KO DMEM) is substituted. Differentwells are then treated with different cocktails of soluble factors thatare candidates for replacing the components of the conditioned medium.Efficacy of each mixture is determined if the treated cells aremaintained and proliferate in a satisfactory manner, optimally as wellas in conditioned medium. Potential differentiation factors orconditions can be tested by treating the cells according to the testprotocol, and then determining whether the treated cell developsfunctional or phenotypic characteristics of a differentiated cell of aparticular lineage.

Feeder-free pPS cultures can also be used for the testing ofpharmaceutical compounds in drug research. Assessment of the activity ofcandidate pharmaceutical compounds generally involves combining thedifferentiated cells of this invention with the candidate compound,determining any resulting change, and then correlating the effect of thecompound with the observed change. The screening may be done, forexample, either because the compound is designed to have apharmacological effect on certain cell types, or because a compounddesigned to have effects elsewhere may have unintended side effects. Twoor more drugs can be tested in combination (by combining with the cellseither simultaneously or sequentially), to detect possible drug-druginteraction effects. In some applications, compounds are screenedinitially for potential toxicity (Castell et al., pp 375-410 in “Invitro Methods in Pharmaceutical Research,” Academic Press, 1997).Cytotoxicity can be determined by the effect on cell viability,survival, and morphology, on the expression or release of certainmarkers, receptors or enzymes, on DNA synthesis or repair, measured by[³H]-thymidine or BrdU incorporation, or on sister chromatid exchange,determined by metaphase spread. The reader is referred generally to thestandard textbook “In vitro Methods in Pharmaceutical Research”,Academic Press, 1997, and U.S. Pat. No. 5,030,015.

Genomics

Suitable methods for comparing expression at the protein level includethe immunoassay or immunocytochemistry techniques described above.Suitable methods for comparing expression at the level of transcriptioninclude methods of differential display of mRNA (Liang et al., CancerRes. 52:6966, 1992), and matrix array expression systems (Schena et al.,Science 270:467, 1995; Eisen et al., Methods Enzymol. 303:179, 1999;Brown et al., Nat. Genet. 21 Suppl 1:33, 1999).

The use of microarray in analyzing gene expression is reviewed generallyby Fritz et al Science 288:316, 2000; “Microarray Biochip Technology”,M. Schena ed., Eaton Publishing Company; “Microarray analysis”, Gwynne &Page, Science (Aug. 6, 1999 supplement); Pollack et al., Nat Genet.23:41, 1999; Gerhold et al., Trends Biochem. Sci. 24:168, 1999; “GeneChips (DNA Microarrays)”, L. Shi at the Internet URL www.Gene-Chips.com.Systems and reagents for performing microarray analysis are availablecommercially from companies such as Affymetrix, Inc., Santa ClaraCalif.; Gene Logic Inc., Columbia Md.; HySeq Inc., Sunnyvale Calif.;Molecular Dynamics Inc., Sunnyvale Calif.; Nanogen, San Diego Calif.;and Synteni Inc., Fremont Calif. (acquired by Incyte Genomics, Palo AltoCalif.).

Solid-phase arrays are manufactured by attaching the probe at specificsites either by synthesizing the probe at the desired position, or bypresynthesizing the probe fragment and then attaching it to the solidsupport. A variety of solid supports can be used, including glasses,plastics, ceramics, metals, gels, membranes, paper, and beads of variouscomposition. U.S. Pat. No. 5,445,934 discloses a method of on-chipsynthesis, in which a glass slide is derivatized with a chemical speciescontaining a photo-cleavable protecting group. Each site is sequentiallydeprotected by irradiation through a mask, and then reacted with a DNAmonomer containing a photoprotective group. Methods for attaching apresynthesized probe onto a solid support include adsorption, ultraviolet linking, and covalent attachment. In one example, the solidsupport is modified to carry an active group, such as hydroxyl,carboxyl, amine, aldehyde, hydrazine, epoxide, bromoacetyl, maleimide,or thiol groups through which the probe is attached (U.S. Pat. Nos.5,474,895 and 5,514,785).

The probing assay is typically conducted by contacting the array by afluid potentially containing the nucleotide sequences of interest undersuitable conditions for hybridization conditions, and then determiningany hybrid formed. For example, mRNA or DNA in the sample is amplifiedin the presence of nucleotides attached to a suitable label, such as thefluorescent labels Cy3 or Cy5. Conditions are adjusted so thathybridization occurs with precise complementary matches or with variousdegrees of homology, as appropriate. The array is then washed, and boundnucleic acid is determined by measuring the presence or amount of labelassociated with the solid phase. Different samples can be comparedbetween arrays for relative levels of expression, optionallystandardized using genes expressed in most cells of interest, such as aribosomal or housekeeping gene, or as a proportion of totalpolynucleotide in the sample. Alternatively, samples from two or moredifferent sources can be tested simultaneously on the same array, bypreparing the amplified polynucleotide from each source with a differentlabel.

An exemplary method is conducted using a Genetic Microsystems arraygenerator, and an Axon Genepix™ Scanner. Microarrays are prepared byfirst amplifying cDNA fragments encoding marker sequences to be analyzedin a 96 or 384 well format. The cDNA is then spotted directly onto glassslides at a density as high as >5,000 per slide. To compare mRNApreparations from two cells of interest, one preparation is convertedinto Cy3-labeled cDNA, while the other is converted into Cy5-labeledcDNA. The two cDNA preparations are hybridized simultaneously to themicroarray slide, and then washed to eliminate non-specific binding. Anygiven spot on the array will bind each of the cDNA products inproportion to abundance of the transcript in the two original mRNApreparations. The slide is then scanned at wavelengths appropriate foreach of the labels, the resulting fluorescence is quantified, and theresults are formatted to give an indication of the relative abundance ofmRNA for each marker on the array.

Identifying expression products for use in characterizing and affectingdifferentiated cells of this invention involves analyzing the expressionlevel of RNA, protein, or other gene product in a first cell type, suchas a pluripotent precursor cell, or a cell capable of differentiatingalong a particular pathway; then analyzing the expression level of thesame product in a control cell type; comparing the relative expressionlevel between the two cell types, (typically normalized by total proteinor RNA in the sample, or in comparison with another gene productexpected to be expressed at a similar level in both cell types, such asa house-keeping gene); and then identifying products of interest basedon the comparative expression level.

Products will typically be of interest if their relative expressionlevel is at least about 2-fold, 10-fold, or 100-fold elevated (orsuppressed) in differentiated pPS cells of this invention, in comparisonwith the control. This analysis can optionally be computer-assisted, bymarking the expression level in each cell type on an independent axis,wherein the position of the mark relative to each axis is in accordancewith the expression level in the respective cell, and then selecting aproduct of interest based on the position of the mark. Alternatively,the difference in expression between the first cell and the control cellcan be represented on a color spectrum (for example, where yellowrepresents equivalent expression levels, red indicates augmentedexpression and blue represents suppressed expression). The product ofinterest can then be selected based on the color representing expressionof one marker of interest, or based on a pattern of colors representinga plurality of markers.

Genes and proteins that undergo a change in expression level duringdifferentiation are of interest for a number of purposes. For example,where expression is high in pPS cells and decreases duringdifferentiation can be used as molecular markers of the undifferentiatedstate. Reagents corresponding to these markers, such as antibodies, canbe used, for example, to eliminate undifferentiated pPS cells from apopulation of differentiated cells by immunoaffinity isolation orcomplement-mediated lysis. Where expression is increased duringdifferentiation, the markers can be used in a similar manner to purify,enrich, remove or eliminate specific cell types derived from pPS cells.These markers may serve as indicators of broad classes of celldifferentiation, such as genes or proteins expressed in mesodermal,endodermal or ectodermal lineages, or may serve as markers of highlydifferentiated cell types.

Genes that are upregulated during expression may also be useful toinfluence the differentiation of pPS cells into specific lineages. Forinstance, the forced expression in undifferentiated pPS cells oftransgenes encoding transcription factors, growth factors, receptors andsignaling molecules can be tested for an ability to influencedifferentiation into specific cell lineages.

Once the sequence of mRNA preferentially expressed or repressed indifferentiated cells is determined, it can be used in the manufacture ofpolynucleotides that contain such sequences, polypeptides they encode,and antibody specific for the polypeptides. Oligonucleotides of lessthan ˜50 base pairs are conveniently prepared by chemical synthesis,either through a commercial service or by a known synthetic method, suchas solid phase synthesis (Hirose et al., Tetra. Lett. 19:2449-2452,1978; U.S. Pat. No. 4,415,732). Polynucleotides can also be manufacturedby PCR amplification using a template with the desired sequence (U.S.Pat. Nos. 4,683,195 and 4,683,202). Production scale amounts of largepolynucleotides are conveniently obtained by inserting the desiredsequence into a suitable cloning vector, and either reproducing theclone, or transfecting the sequence into a suitable host cell. Shortpolypeptides can be prepared by solid-phase chemical synthesis: seeDugas & Penney, Bioorganic Chemistry, Springer-Verlag NY pp 54-92(1981). Longer polypeptides are conveniently manufactured by translationin an in vitro translation system, or by expression in a suitable hostcell (U.S. Pat. No. 5,552,524). Polyclonal and monoclonal antibodyspecific for polypeptides encoded by mRNA and cDNA of this invention canbe obtained by determining amino acid sequence from a protein encodingregion in an expression library, and immunizing an animal or contactingan immunocompetent cell or particle with a protein containing thedetermined sequence, according to standard techniques.

Therapeutic Compositions

Differentiated cells of this invention can also be used for tissuereconstitution or regeneration in a human patient in need thereof. Thecells are administered in a manner that permits them to graft to theintended tissue site and reconstitute or regenerate the functionallydeficient area.

In one example, neural stem cells are transplanted directly intoparenchymal or intrathecal sites of the central nervous system,according to the disease being treated. Grafts are done using singlecell suspension or small aggregates at a density of 25,000-500,000 cellsper μL (U.S. Pat. No. 5,968,829). The efficacy of neural celltransplants can be assessed in a rat model for acutely injured spinalcord as described by McDonald et al. (Nat. Med. 5:1410, 1999. Asuccessful transplant will show transplant-derived cells present in thelesion 2-5 weeks later, differentiated into astrocytes,oligodendrocytes, and/or neurons, and migrating along the cord from thelesioned end, and an improvement in gate, coordination, andweight-bearing.

The efficacy of cardiomyocytes can be assessed in an animal model forcardiac cryoinjury, which causes 55% of the left ventricular wall tissueto become scar tissue without treatment (Li et al., Ann. Thorac. Surg.62:654, 1996; Sakai et al., Ann. Thorac. Surg. 8:2074, 1999, Sakai etal., J. Thorac. Cardiovasc. Surg. 118:715, 1999). Successful treatmentwill reduce the area of the scar, limit scar expansion, and improveheart function as determined by systolic, diastolic, and developedpressure. Cardiac injury can also be modeled using an embolization coilin the distal portion of the left anterior descending artery (Watanabeet al., Cell Transplant. 7:239, 1998), and efficacy of treatment can beevaluated by histology and cardiac function. Cardiomyocyte preparationsembodied in this invention can be used in therapy to regenerate cardiacmuscle and treat insufficient cardiac function (U.S. Pat. No. 5,919,449and WO 99/03973).

Hepatocytes and hepatocyte precursors can be assessed in animal modelsfor ability to repair liver damage. One such example is damage caused byintraperitoneal injection of D-galactosamine (Dabeva et al., Am. J.Pathol. 143:1606, 1993). Efficacy of treatment can be determined byimmunocytochemical staining for liver cell markers, microscopicdetermination of whether canalicular structures form in growing tissue,and the ability of the treatment to restore synthesis of liver-specificproteins. Liver cells can be used in therapy by direct administration,or as part of a bioassist device that provides temporary liver functionwhile the subject's liver tissue regenerates itself following fulminanthepatic failure.

Cells prepared according to this invention that are useful for human orveterinary therapy are optimally supplied in a pharmaceuticalcomposition, comprising an isotonic excipient prepared undersufficiently sterile conditions for human administration. For generalprinciples in medicinal formulation, the reader is referred to CellTherapy: Stem Cell Transplantation, Gene Therapy, and CellularImmunotherapy, by G. Morstyn & W. Sheridan eds, Cambridge UniversityPress, 1996; and Hematopoietic Stem Cell Therapy, E. D. Ball, J. Lister& P. Law, Churchill Livingstone, 2000. The compositions may be packagedwith written instructions for use of the cells in tissue regeneration,or restoring a therapeutically important metabolic function.

The examples that follow are provided by way of further illustration,and are not meant to imply any limitation in the practice of the claimedinvention.

EXAMPLES Example 1 Feeder-Free Passage of hES Cells

Undifferentiated hES cells isolated on primary mouse embryonic feedercells were propagated in the absence of feeder cells. The culture wellswere coated with Matrigel®, and the cells were cultured in the presenceof conditioned nutrient medium obtained from a culture of irradiatedprimary fibroblasts.

Preparation of Conditioned Media (CM) from Primary Mouse EmbryonicFibroblasts (mEF):

Fibroblasts were harvested from T150 flasks by washing once withCa⁺⁺/Mg⁺⁺ free PBS and incubating in 1.5-2 mL trypsin/EDTA (Gibco) forabout 5 min. After the fibroblasts detached from the flask, they werecollected in mEF media (DMEM+10% FBS). The cells were irradiated at 4000rad (508 sec at 140 kV: shelf setting 6 in a Torrex generator), countedand seeded at about 55,000 cells cm⁻² in mEF media (525,000 cells/wellof a 6 well plate). After at least 4 hours the media were exchanged withSR containing ES media, using 3-4 mL per 9.6 cm well of a 6 well plate.Conditioned media was collected daily for feeding of hES cultures.Alternatively, medium was prepared using mEF plated in culture flasks,exchanging medium daily at 0.3-0.4 mL cm⁻². Before addition to the hEScultures, the conditioned medium was supplemented with 4 ng/mL of humanbFGF (Gibco). Fibroblast cultures were used in this system for about 1week, before replacing with newly prepared cells.

Matrigel® Coating:

Growth Factor Reduced Matrigel® or regular Matrigel® (Becton-Dickinson,Bedford Mass.) was thawed at 4° C. The Matrigel® was diluted 1:10 to1:500 (typically 1:30) in cold KO DMEM. 0.75-1.0 mL of solution wasadded to each 9.6 cm² well, and incubated at room temperature for 1 h,or at 4° C. at least overnight. The coated wells were washed once withcold KO DMEM before adding cells. Plates were used within 2 h aftercoating, or stored in DMEM at 4° C. and used within ˜1 week.

Human ES Culture:

Undifferentiated hES colonies were harvested from hES cultures onfeeders as follows. Cultures were incubated in ˜200 U/mL collagenase IVfor about 5 minutes at 37° C. Colonies were harvested by pickingindividual colonies up with a 20 μL pipet tip under a microscope or byscraping and dissociating into small clusters in conditioned medium(CM). These cells were then seeded onto Matrigel® in conditioned mediaat 15 colonies to each 9.6 cm² well (if 1 colony is ˜10,000 cells, thenthe plating density is ˜15,000 cells cm⁻²).

The day after seeding on Matrigel®, hES cells were visible as smallcolonies (˜100-2,000 cells) and there were cells in between the coloniesthat appeared to be differentiating or dying. As the hES cellsproliferated, the colonies became quite large and very compact,representing the majority of surface area of the culture dish. The hEScells in the colonies had a high nucleus to cytoplasm ratio and hadprominent nucleoli, similar to hES cells maintained on feeder cells. Atconfluence, the differentiated cells in between the colonies representedless than 10% of the cells in the culture.

Six days after seeding, the cultures had become almost confluent. Thecultures were split by incubating with 1 mL ˜200 U/mL Collagenase IVsolution in KO DMEM for ˜5 minutes at 37° C. The collagenase solutionwas aspirated, 2 mL hES medium was added per well, and the hES cellswere scraped from the dish with a pipette. The cell suspension wastransferred to a 15 mL conical tube, brought up to a volume of 6 mL, andgently triturated to dissociate the cells into small clusters of 10-2000cells. The cells were then re-seeded on Matrigel® coated plates in CM,as above. Cells were seeded at a 1:3 or 1:6 ratio, approximately 90,000to 170,000 cells cm⁻², making up the volume in each well to 3 mL. Mediumwas changed daily, and the cells were split and passaged again at 13 dand again at 19 d after initial seeding.

Undifferentiated hES cells express SSEA-4, Tra-1-60, Tra-1-81, OCT-4,and hTERT. In order to assess whether the cells maintained infeeder-free conditions retained these markers, cells were evaluated byimmunostaining, reverse transcriptase PCR amplification, and assay fortelomerase activity. As assayed by fluorescence-activated cell sorting,cells on Matrigel®, laminin, fibronectin or collagen IV expressedSSEA-4, Tra-1-60 and Tra-1-81. There was very little expression ofSSEA-1, a glycolipid that is not expressed by undifferentiated hEScells. Immunocytochemistry analysis shows that SSEA-4, Tra-1-60,Tra-1-81, and alkaline phosphatase were expressed by the hES colonies onMatrigel® or laminin, as seen for the cells on feeders—but not by thedifferentiated cells in between the colonies.

FIG. 1 shows OCT-1 and hTERT expression of H1 cells on feeders and offfeeders, as detected by reverse-transcriptase PCR amplification. Forradioactive relative quantification of individual gene products,QuantumRNA™ Alternate18S Internal Standard primers (Ambion, Austin Tex.,USA) were employed according to the manufacturer's instructions.Briefly, the linear range of amplification of a particular primer pairwas determined, then coamplified with the appropriate mixture ofalternate18S primers:competimers to yield PCR products with coincidinglinear ranges. Before addition of AmpliTaq™ (Roche) to PCR reactions,the enzyme was pre-incubated with the TaqStart™ antibody (ProMega)according to manufacturer's instructions. Radioactive PCR reactions wereanalyzed on 5% non-denaturing polyacrylamide gels, dried, and exposed tophosphoimage screens (Molecular Dynamics) for 1 hour. Screens werescanned with a Molecular Dynamics Storm 860 and band intensities werequantified using ImageQuant™ software. Results are expressed as theratio of radioactivity incorporated into the hTERT or OCT-4 band,standardized to the radioactivity incorporated into the 18s band.

Primers and amplification conditions for particular markers are asfollows. OCT-4: Sense (SEQ. ID NO:1) 5′-CTTGCTGCAG AAGTGGGTGG AGGAA-3′;Antisense (SEQ. ID NO:2) 5′-CTGCAGTGTG GGTTTCGGGC A-3′;alternate18:competimers 1:4; 19 cycles (94° 30 sec; 60° 30 sec; 72° 30sec). hTERT: Sense (SEQ. ID NO:3) 5′-CGGAAGAGTG TCTGGAGCAA-3′; Antisense(SEQ. ID NO:4) 5′-GGATGAAGCG GAGTCTGGA-3′; alternate18:competimers 1:12;34 cycles (94° 30 sec; 60° 30 sec; 72° 30 sec).

The transcription factor OCT-4 is normally expressed in theundifferentiated hES cells and is down-regulated upon differentiation.The cells maintained on Matrigel® or laminin in conditioned medium (CM)for 21 days express OCT-4, whereas cells maintained in Matrigel® inunconditioned regular medium (RM) did not. Cells maintained onfibronectin or collagen IV, which showed a large degree ofdifferentiation, expressed lower levels of OCT-4 compared to cells onfeeders, Matrigel® or laminin.

Telomerase activity was measured by TRAP assay (Kim et al., Science266:2011, 1997; Weinrich et al., Nature Genetics 17:498, 1997). All thecultures conditions showed positive telomerase activity after 40 days onMatrigel®, laminin, fibronectin or collagen IV in mEF conditionedmedium.

Example 2 Direct Differentiation of hES Cells

Differentiation using standard methods of aggregate formation wascompared with a technique of this invention in which cells aredifferentiated by plating directly onto a solid surface under certainconditions.

For the aggregate differentiation technique, monolayer cultures ofrhesus and human ES lines were harvested by incubating in Collagenase IVfor 5-20 min, and the cells were scraped from the plate. The cells werethen dissociated and plated in non-adherent cell culture plates inFBS-containing medium (20% non-heat-inactivated FBS (Hyclone),supplemented with 0.1 mM non-essential amino acids, 1 mM glutamine, 0.1mM β-mercaptoethanol. The EBs were fed every other day by the additionof 2 mL of medium per well (6 well plate). When the volume of mediumexceeded 4 mL/well, the EBs were collected and resuspended in freshmedium. The plates were placed into a 37° C. incubator, and in someinstances, a rocker was used to facilitate maintaining aggregates insuspension. After 4-8 days in suspension, aggregate bodies formed andwere plated onto a substrate to allow for further differentiation.

For the direct differentiation technique, suspensions of rhesus andhuman ES cells were prepared in a similar fashion. The cells were thendissociated by trituration to clusters of ˜50-100 cells, and plated ontoglass coverslips treated with poly-ornithine. The cells were maintainedin serum containing medium, or defined medium for 7-10 days beforeanalysis. Cells were tested by immunoreactivity for β-tubulin III andMAP-2, which are characteristic of neurons, and glial fibrillary acidicprotein (GFAP), which is characteristic of astrocytes.

Six different ES lines differentiated into cells bearing markers forneurons and astrocytes, using either the aggregate or directdifferentiation technique. In cultures derived from rhesus ES cells,percentage of aggregates that contained neurons ranged from 49% to 93%.In cultures derived from human ES cells, the percentage of aggregatescontaining neurons ranged from 60% to 80%. Double labeling for GABA andβ-tubulin indicated that a sub-population of the neurons express theinhibitory neurotransmitter GABA. Astrocytes and oligodendrocytes wereidentified with GFAP immune reactivity and GalC immune reactivity,respectively. Therefore, the human and rhesus ES cells have the capacityto form all three major cell phenotypes in the central nervous system.

The effect of several members of the neurotrophin growth factor familywas examined. hES cells were differentiated by harvesting withcollagenase, dissociating, and reseeding onto poly-ornithine coatedcover slips. The cells were plated into DMEM/F12+N2+10% FBS overnight.The following day, the serum was removed from the medium and replacedwith 10 ng/mL human bFGF and the growth factor being tested. After 24hours, bFGF was removed from the medium. These cultures were fed everyother day. They were fixed after 7 days of differentiation andimmunostained for analysis. The number of neurons was evaluated bycounting cells positive for β-tubulin. Cultures maintained in thepresence of 10 ng/mL brain derived neurotrophic factor (BDNF) formedapproximately 3-fold more neurons than the control cultures. Culturesmaintained in neurotrophin-3 (1 ng/mL) formed approximately 2-fold moreneurons than control cultures.

To assess cardiomyocyte formation, EBs were transferred togelatin-coated plates or chamber slides after 4 days in the suspensioncultures. The EBs attached to the surface after seeding, proliferatedand differentiated into different types of cells. Spontaneouslycontracting cells were observed in various regions of the culture atdifferentiation day 8 and the number of beating regions increased untilabout day 10. In some cases, more than 75% of the EBs had contractingregions. Beating cells were morphologically similar to mouse EScell-derived beating cardiomyocytes. In these cultures 100% of thecontracting areas were immunoreactive with cardiac troponin I (cTnI),while minimal immunoreactivity was observed in the non-beating cells.

Cultures of differentiated EBs were subjected to Western blot analysisusing monoclonal antibody against cTnI. This assay gave a strong 31 kDaprotein signal, corresponding to the size of the purified native humancTnI. It was detected in differentiated human ES cells containingcontracting cells, but not in undifferentiated ES cells ordifferentiated cultures with no evidence of contracting cells. As acontrol, the blot was reprobed with β-actin specific antibody,confirming the presence of similar amounts of proteins in all samples.

In other experiments, EBs were cultured for 8 or 16 days and maintainedas adherent cultures for an additional 10 days. RNA was prepared fromthe differentiated human ES cells and semiquantitative RT-PCR wasperformed to detect the relative expression of the endoderm-specificproducts α₁-anti-trypsin, AFP, and albumin. Low levels ofα₁-anti-trypsin and AFP were detected in the undifferentiated cultures;little or no albumin was detected in the same cultures. All 3 markerswere detected at significantly higher levels after differentiation.Expression of all 3 endoderm markers was higher in cultures derived from8 day embryoid bodies than 16 day embryoid bodies.

Example 3 Direct Differentiation of hES to Hepatocyte-Like Cells WithoutForming Embryoid Bodies

This experiment demonstrated the use of the direct differentiationtechnique for deriving human ES cells into a relatively uniformpopulation of cells with phenotypic markers of hepatocytes.

The hES cells were maintained in undifferentiated culture conditions(Matrigel® plus mEF conditioned medium) for 2-3 days after splitting. Atthis time, the cells were 50-60% confluent and the medium was exchangedwith unconditioned SR medium containing 1% DMSO.

The cultures were fed daily with SR medium for 4 days and then exchangedinto unconditioned SR medium containing 2.5% Na-butyrate (which waspreviously identified as a hepatocyte differentiation agent). Thecultures were fed daily with this medium for 6 days; at which time onehalf of the cultures were evaluated by immunocytochemistry. The otherhalf of the cultures were harvested with trypsin and replated ontocollagen, to further promote enrichment for hepatocyte lineage cells.Immunocytochemistry was then performed on the following day.

As shown in Table 1, the cells which underwent the final re-plating had˜5-fold higher albumin expression, similar α₁-antitrypsin expression and2-fold less cytokeratin expression than the cells not re-plated. Thesecondary plating for the cells is believed to enrich for thehepatocyte-like cells.

TABLE 1 Phenotype of Differentiated Cells No trypsinizationTrypsinization Antibody Specificity % positive % positive (no primaryantibody) 0  0  (IgG1 control) 0  0  albumin   11% 63%α₁-antitrypsin >80% >80%   α-fetoprotein 0  0  Cytokeratin 8 >80% 45%Cytokeratin 18 >80% 30% Cytokeratin 19 >80% 30% glycogen 0  >50%  

Adjustments to culture conditions are shown in Table 2. HepatocyteCulture Medium is purchased from Clonetics; Strom's Medium is preparedas described in Runge et al., Biochem. Biophys. Res. Commun. 265:376,1999. The cell populations obtained are assessed by immunocytochemistryand enzyme activity.

TABLE 2 Direct Differentiation Protocols Undifferentiated cellsPre-differentiation Hepatocyte induction Further differentiation (untilconfluent) (4 days) (6 days) (Groups 1-3 only; 4 days) Feeder-free 20%SR medium + 20% SR medium + HCM + 30 ng/mL hEGF + conditions 1% DMSO 1%DMSO + 10 ng/mL TGF-α + 2.5 mM butyrate 30 ng/mL HGF + 1% DMSO + 2.5 mMbutyrate Feeder-free 20% SR medium + 20% SR medium + 20% SR medium +conditions 1% DMSO 1% DMSO + 30 ng/mL hEGF + 2.5 mM butyrate 10 ng/mLTGF-α + 30 ng/mL HGF + 1% DMSO + 2.5 mM butyrate Feeder-free 20% SRmedium + 20% SR medium + Strom's medium + conditions 1% DMSO 1% DMSO +30 ng/mL hEGF + 2.5 mM butyrate 10 ng/mL TGF-α + 30 ng/mL HGF + 1%DMSO + 2.5 mM butyrate Feeder-free 20% SR medium + HCM + 30 ng/mL hEGF +conditions 1% DMSO 10 ng/mL TGF-α + 30 ng/mL HGF + 1% DMSO + 2.5 mMbutyrate Feeder-free 20% SR medium + 20% SR medium + conditions 1% DMSO30 ng/mL hEGF + 10 ng/mL TGF-α + 30 ng/mL HGF + 1% DMSO + 2.5 mMbutyrate Feeder-free 20% SR medium + Strom's medium + conditions 1% DMSO30 ng/mL hEGF + 10 ng/mL TGF-α + 30 ng/mL HGF + 1% DMSO + 2.5 mMbutyrate Feeder-free HCM + 30 ng/mL hEGF + HCM + 30 ng/mL hEGF +conditions 10 ng/mL TGF-α + 10 ng/mL TGF-α + 30 ng/mL HGF + 30 ng/mLHGF + 1% DMSO 1% DMSO + 2.5 mM butyrate Feeder-free 20% SR medium + 20%SR medium + conditions 30 ng/mL hEGF + 30 ng/mL hEGF + 10 ng/mL TGF-α +10 ng/mL TGF-α + 30 ng/mL HGF + 30 ng/mL HGF + 1% DMSO 1% DMSO + 2.5 mMbutyrate Feeder-free Strom's medium + Strom's medium + conditions 30ng/mL hEGF + 30 ng/mL hEGF + 10 ng/mL TGF-α + 10 ng/mL TGF-α + 30 ng/mLHGF + 30 ng/mL HGF + 1% DMSO 1% DMSO + 2.5 mM butyrateOther additives tested in the subsequent (4-day) maturation step includefactors such as FGF-4, and oncostatin M in the presence ofdexamethazone.

FIG. 2 shows the effect of HCM on maturation of hES-derived cells. Leftcolumn: 10× magnification; Right column: 40× magnification. By 4 days inthe presence of butyrate, more than 80% of cells in the culture arelarge in diameter, containing large nuclei and granular cytoplasm (RowA). After 5 days in SR medium, the cells were switched to HCM. Two dayslater, many cells are multinucleated, and have a large polygonal shape(Row B). By 4 days in HCM, multinucleated polygonal cells are common,and have a darker cytosol (Row C), by which criteria they resemblefreshly isolated human adult hepatocytes (Row D) or fetal hepatocytes(Row E).

Example 4 Microarray Analysis of Expression by Undifferentiated andDifferentiated Cells

An analysis of differential gene expression was performed by contrastingmRNA from undifferentiated H9 cultures with mRNA from corresponding EBs.The EBs were maintained in growth medium for 8 days, or kept in growthmedium for 4 days, followed by 4 days of treatment with 0.5 μM retinoicacid. EBs were harvested after 2 d, 4 d, or 8 d and the resulting mRNAwas compared directly with mRNA from undifferentiated cultures. Thisanalysis tracks the transformation of a relatively homogenous cellpopulation into a complex mix of differentiated cell types, and thus thereadouts are affected both by the magnitude of the change in geneexpression, and, in the case of expression changes specific to adifferentiated cell type, by the representation of that cell type in theculture. The arrays used in these experiments sample approximately10,000 cDNAs selected to represent a large portion of characterizedhuman genes.

Total RNA was harvested from human ES cultures or their differentiatedderivatives using the Qiagen RNAeasy™ Miniprep kit according to themanufacturer's instructions. RNA was quantified by measuring ultravioletabsorption at 260 nm. Poly A⁺ mRNA was prepared from the total RNApreparations using Qiagen Oligotex™ Minipreps according to theinstructions of the manufacturer. Final mRNA preparations werequantified by A₂₆₀ measurements, then visually inspected followingelectrophoresis on native agarose gels. Sample RNAs were sent to acontract laboratory (Incyte Pharmaceuticals, Palo Alto, Calif.) forconversion into Cy3- or Cy5 labeled cDNA probe, which was subsequentlyhybridized to UNIGEM™ 1.0 arrays.

Following processing of the hybridized arrays, fluorescence measurementswere quantified and the results returned for analysis. Probe pairingswere performed with samples from undifferentiated ES cells in the Cy3channel, and the differentiated ES cell samples in the Cy5 channel. Achange in expression (as measured by comparing the Cy3 and Cy5 channels)was generally considered significant if the difference was at least2.5-fold.

FIG. 3 shows the expression analysis of embryoid body (EB) cells. Thenumbers in the matrix compare expression at the mRNA level withexpression in the undifferentiated hES cell line from which the EBs werederived. Numbers 1.1 and above represent a proportional increase inexpression in EB cells; numbers −1.1 and below represent a proportionaldecrease in expression. The four columns show results obtained from EBsin standard suspension culture for 2, 4, or 8 days; or cultured 4 daysin regular medium and 4 days in medium containing retinoic acid(4d−/4d+).

The differentiation of hES cells involves the activation and repressionof many genes, including ESTs with no known function. Interestingly, theaddition of retinoic acid to the suspension culture for the final 4 daysof differentiation had relatively minor effect on the gene expressionpattern (compare 4d−/4d+ with 8d).

Genes whose expression is reduced during differentiation sample a widerange of functions, including metallothioneins, growth factors (e.g.,FGF9), secreted cysteine-rich proteins (e.g., osteopontin, AGF-BP5,Cyr61, connective tissue growth factor), the selenium donor proteinselD, and many others. In general, the most significant alterations inexpression occur after 4 days of suspension culture, and correspond withthe onset of changes in cell morphologies. Of interest, the expressionof two genes involved in the catabolism of α-D-Glucose phosphate,UDP-glucose phosphorylase and phosphoglucomutase, are dramaticallyreduced upon differentiation, suggesting a potential alteration inglucose metabolism.

The arrays used in these experiments do not contain cDNA featurescorresponding to hTERT; however, a marked decrease in the expression ofthe mRNA for TRF1 was observed. TRF1 is a principal telomere bindingfactor whose expression has been correlated with a shortening oftelomere lengths. Thus, the expression of both positive (hTERT) andnegative (TRF1) regulators of telomere length is reduced during ES celldifferentiation.

Several genes associated with visceral endoderm and early hepaticdifferentiation were predominant in this analysis, includingα-fetoprotein, apoplipoprotein A-II, apoplipoprotein AI regulatoryprotein-1, α₁-antitrypsin, and the α, β, and γ chains of fibrinogen.This induction is apparent within 2 days of differentiation, and is notsubstantially affected by retinoid treatment. The induced expression ofcellular retinoic acid binding proteins 1 and 2 (CRABP I, II) is notobserved in retinoid treated cultures, consistent with a proposednegative feedback loop in which retinoids specifically inhibit thetranscription of the promoter of the CRAB I gene.

Expression of the IL-6 receptor gp130 is low in hES cultures, and isinduced upon differentiation. These results provide a molecular basisfor the lack of LIF responsiveness in hES cultures (Thomson et al.,1999; Reubinoff et al., 2000) and indicate a substantially differentrole for gp130 in human vs. mouse ES cells, where LIF signaling isdirectly implied in the maintenance of the undifferentiated state.

Other differentiation-induced genes include the protein homologspleiotropin and midkine. These secreted cytokine have proposed roles asmitogens for neuronal and hepatic cell types, or as generalizedangiogenic factors (Owada et al., 1999; Sato et al., 1999), and as suchmay play a similar role in ES cell differentiation. The induction of DNAbinding proteins, such as homeobox b5 protein and meis1, likely reflectsthe central role of transcriptional regulators in differentiationprocesses.

Example 5 Direct Differentiation of hES Cells to Neurons

This study evaluated various paradigms for differentiating human EScells into neurons without the formation of embryoid bodies.

A strategy was developed in which the test factors were placed intogroups based on homology and/or functional redundancy (Table 3).Grouping factors increases the likelihood that an activity associatedwithin that group will be elicited on the ES cell population. Thehypothesis is that certain factors within the mixture will initiate adifferentiation cascade. As differentiation proceeds, and the receptorexpression profile of the cells change, they will become responsive toother factors in the mixture.

Providing a complex mixture of factors continuously over the treatmentperiod avoids the need to define exactly how and when the responsivenessof the cells changes. When a mixture is identified that elicits thedesired differentiation process, it can be systematically simplified toachieve a minimal optimal mixture. After further testing, minimaltreatment may ultimately comprise one, two, three, or more of thefactors listed, used either simultaneously or in sequence according tothe empirically determined protocol.

TABLE 3 Test Factor Groups Group 1 Group 2 Group 3 NeurotrophinsMitogens Stem Cell Factors 30 ng/mL NGF 30 ng/mL EGF  8 ng/mL LIF 30ng/mL NT-3 30 ng/mL FGF-2  3 ng/mL IL-6 30 ng/mL NT-4 37 ng/mL FGF-8b  3ng/mL IL-11 30 ng/mL BDNF 30 ng/mL IGF-I  3 ng/mL SCF 30 ng/mL PDGF-AA30 ng/mL CNTF Group 4 Group 5 Group 6 Differentiation Factors TGF-βSuperfamily Differentiation TGF-β Superfamily Antagonists Factor 30ng/mL BMP-2 150 ng/mL Noggin 37 ng/mL SHH 37 ng/mL GDF-5  30 ng/mLFollistatin  3 ng/mL GDNF 30 ng/mL Neurturin Group 7 Group 8 Group 9Neurotrophic Differentiation Survival Factor Factor Factor/Antioxidant37 ng/mL Midkine 17 μM Retinoic Acid 166 μM Ascorbic Acid Group 10Differentiation Factor/ Group 11 Neurotransmitter Survival Factor 10 μMDopamine 100 μM Dibutyryl cAMP

The experiment was conducted as follows. Monolayer cultures of a humanES cell line were harvested by incubating in Collagenase IV for 5-10min, and then scraping the cells from the plate. The cells weredissociated by trituration and plated at subconfluence onto 96 welltissue culture plates pretreated with growth factor-reduced Matrigel® inKnockout DMEM medium (Gibco BRL) with Knockout Serum Replacement (GibcoBRL) conditioned 24 h by mouse embryonic fibroblasts. One day afterplating, the medium was replaced with Neurobasal Medium (Gibco BRL)supplemented with 1 mM glutamine, B27 supplement (Gibco BRL) and groupsof test factors as described below. The cells were fed daily with freshNeurobasal Medium containing glutamine, B27, and test factors for 11days.

After 11 days, the cells were harvested by incubation in trypsin for5-10 min, replated at a 1:6 dilution onto 96 well tissue culture platespretreated with laminin, and fed daily with fresh Neurobasal Mediumcontaining glutamine, B27 and test factors for an additional 5 days.Cells were fixed for 20 min in 4% paraformaldehyde, and stained withantibodies to the early neuronal marker, β-Tubulin-III, the lateneuronal marker, MAP-2, and tyrosine hydroxylase, an enzyme associatedwith dopaminergic neurons. Cell nuclei were labeled with DAPI, andquantified by visual inspection. Results are shown in Table 4.

TABLE 4 Direct Differentiation of hES Cells to Neurons TyrosineβTubulin-III Hydroxylase positive MAP-2 positive Test Compound GroupsCells/ positive Cells/ Included in Cell Culture Well % Total Cells/WellWell % Total Control 102 — 2 1 — Treatment A: 1, 2, 3, 4, 6, 7, 8, 9,10, 11 0 0 0 0 — Treatment B: 1, 2, 3, 5, 6, 7, 8, 9, 10, 11 362  6% 13214 0.2% Treatment C: 1, 2, 4, 6, 7, 8, 9, 10, 11 — — — — — Treatment D:1, 2, 5, 6, 7, 8, 9, 10, 11 378 11% 162 16 0.5% Treatment E: 1, 3, 4, 6,7, 8, 9, 10, 11 6 — 2 4 — Treatment F: 1, 3, 5, 6, 7, 8, 9, 10, 11 28212% 92 4 0.2% Treatment G: 1, 4, 6, 7, 8, 9, 10, 11 17 — 0 2 — — = notdetermined

In another experiment, cells were cultured in Neurobasal mediumsupplemented with glutamine, B27 and groups of test factors as before,harvested with trypsin at 8 days, and replated for 5 days. Results areshown in Table 5.

TABLE 5 Direct Differentiation of hES Cells to Neurons Tyrosine Percentof MAP-2 βTubulin-III MAP-2 Hydroxylase positive cells Test CompoundGroups positive positive positive also positive Included in Cell CultureCells/Well Cells/Well Cells/Well for TH Control 4 4 0 Treatment A: 1, 2,3, 4, 6, 7, 8, 9, 10, 11 12 8 3 Treatment B: 1, 2, 3, 5, 6, 7, 8, 9, 10,11 268 12 4 Treatment C: 1, 2, 4, 6, 7, 8, 9, 10, 11 12 0 0 Treatment D:1, 2, 5, 6, 7, 8, 9, 10, 11 372 48 7 15% Treatment E: 1, 3, 4, 6, 7, 8,9, 10, 11 0 0 0 Treatment F: 1, 3, 5, 6, 7, 8, 9, 10, 11 196 56 0Treatment G: 1, 4, 6, 7, 8, 9, 10, 11 16 0 9

Several treatment paradigms induced the direct differentiation ofneurons. Treatments that included Group 5 factors (noggin andfollistatin) were the most effective.

FIG. 4 shows exemplary fields of differentiated cells obtained usingTreatment B, Treatment D, and Treatment F, and stained forβ-tubulin-III. About 5-12% of the cells are neurons, based on morphologyand β-tubulin-III staining. About ⅓ of these are mature neurons, basedon MAP-2 staining. About 2-5% of total neurons (5-15% of MAP-2 positiveneurons) also stained for tyrosine hydroxylase, which is consistent witha dopaminergic phenotype.

It will be recognized that the compositions and procedures provided inthe description can be effectively modified by those skilled in the artwithout departing from the spirit of the invention embodied in theclaims that follow.

1.-14. (canceled)
 15. A method for producing a population of cellscomprising cells that express tyrosine hydroxylase comprising: a)plating and culturing undifferentiated primate pluripotent stem (pPS)cells on a solid surface so that they differentiate without formingembryoid bodies; b) culturing the plated cells in a medium containingnoggin and/or follistatin thereby producing a population of cellsexpressing tyrosine hydroxylase.
 16. The method of claim 15, wherein thepPS cells are plated on a solid surface without any extracellularmatrix.
 17. The method of claim 15, wherein the solid surface comprisesa polycation.
 18. The method of claim 17, wherein the polycation ispolyornithine or polylysine.
 19. The method of claim 15, wherein themedium contains a neurotrophin.
 20. The method of claim 19, wherein theneurotrophin is neurotrophin 3 (NT-3) or brain-derived neurotrophicfactor (BDNF).
 21. The method of claim 15, wherein the primatepluripotent stem cells are human cells expressing the markers stagespecific antigen 3 (SSEA3), stage specific antigen 4 (SSEA4), andmarkers detectable using the antibodies designated Tra-1-60 andTra-1-81.
 21. A method for producing a population of cells comprisingcells that express β-tubullin III comprising: b) culturing primatepluripotent stem cells in a medium containing a neurotrophin therebyproducing a population of cells expressing β-tubullin III.
 22. Themethod of claim 21, wherein the primate pluripotent stem cells areplated and cultured on a solid surface so that they differentiatewithout forming embryoid bodies.
 23. The method of claim 21 wherein theprimate pluripotent stem cells are human cells expressing the markersstage specific antigen 3 (SSEA3), stage specific antigen 4 (SSEA4), andmarkers detectable using the antibodies designated Tra-1-60 andTra-1-81.
 24. The method of claim 21, wherein the neurotrophin isneurotrophin
 3. 25. The method of claim 21, wherein the neurotrophin isbrain derived neurotrophic factor.